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  Topic: A Separate Thread for Gary Gaulin, As big as the poop that does not look< Next Oldest | Next Newest >  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Nov. 17 2016,19:58   

Quote
That's more like it. You do need much more than that simple illustration to show what went where.

That "simple" illustration (actually, it's not that simple) shows quite adequately why your initial assertions are wrong.  If it's that simple, how come you don't understand it?

The additional stuff comprises fascinating additional new details, which also show that you are wrong, and which add greatly to the first diagram but do not contradict it.

Learn the basics, incorporate the information into your thinking, and then you can move on to more complex stuff. So far you have shown yourself to be incapable of the baby steps.

  
GaryGaulin



Posts: 5385
Joined: Oct. 2012

(Permalink) Posted: Nov. 17 2016,22:46   

Quote (N.Wells @ Nov. 17 2016,19:58)
Quote
That's more like it. You do need much more than that simple illustration to show what went where.

That "simple" illustration (actually, it's not that simple) shows quite adequately why your initial assertions are wrong.  If it's that simple, how come you don't understand it?

You only helped prove my point that it's not as simple as you have been making it seem by making both chimp "cousins" who are neatly out on a branch of their own.

--------------
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

   
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Nov. 18 2016,01:55   

Quote (GaryGaulin @ Nov. 17 2016,22:46)
 
Quote (N.Wells @ Nov. 17 2016,19:58)
 
Quote
That's more like it. You do need much more than that simple illustration to show what went where.

That "simple" illustration (actually, it's not that simple) shows quite adequately why your initial assertions are wrong.  If it's that simple, how come you don't understand it?

You only helped prove my point that it's not as simple as you have been making it seem by making both chimp "cousins" who are neatly out on a branch of their own.

No.  Complex details notwithstanding, they are out on a branch of their own.  Your claims were that bonobos aren't chimps, that common chimps are farther from humans than bonobos are, and that bonobos and common chimps are not very close.  Those claims are rubbish.
 
Quote
Whatever helps unseat chimps from their undeserved reputation of being our closest relative is now of service to science.
....................
from what I can see the differences between bonobos and chimps are similar to chimps and gorillas.
 

Those assertions are wrong.  Perhaps inconveniently, bonobos can still legitimately be referred to as a type of chimpanzee.   Bonobos and common chimps are genetically equidistant from us, although we don't know whether our last common ancestor was more like Lucy, Pan paniscus, or Pan troglodytes, and they are genetically more similar to each other than either are to us or to gorillas.  Pan paniscus and Pan troglodytes are a sister group.

  
Texas Teach



Posts: 2084
Joined: April 2007

(Permalink) Posted: Nov. 18 2016,05:42   

Quote (GaryGaulin @ Nov. 17 2016,22:46)
Quote (N.Wells @ Nov. 17 2016,19:58)
Quote
That's more like it. You do need much more than that simple illustration to show what went where.

That "simple" illustration (actually, it's not that simple) shows quite adequately why your initial assertions are wrong.  If it's that simple, how come you don't understand it?

You only helped prove my point that it's not as simple as you have been making it seem by making both chimp "cousins" who are neatly out on a branch of their own.

Gary, this is stuff we teach in school.  No one is hiding the information from you.  Try learning something before shooting your mouth off.

--------------
"Creationists think everything Genesis says is true. I don't even think Phil Collins is a good drummer." --J. Carr

"I suspect that the English grammar books where you live are outdated" --G. Gaulin

  
GaryGaulin



Posts: 5385
Joined: Oct. 2012

(Permalink) Posted: Nov. 18 2016,18:21   

Quote (Texas Teach @ Nov. 18 2016,05:42)
Quote (GaryGaulin @ Nov. 17 2016,22:46)
 
Quote (N.Wells @ Nov. 17 2016,19:58)
 
Quote
That's more like it. You do need much more than that simple illustration to show what went where.

That "simple" illustration (actually, it's not that simple) shows quite adequately why your initial assertions are wrong.  If it's that simple, how come you don't understand it?

You only helped prove my point that it's not as simple as you have been making it seem by making both chimp "cousins" who are neatly out on a branch of their own.

Gary, this is stuff we teach in school.  No one is hiding the information from you.  Try learning something before shooting your mouth off.

If you know so much then you should be able to spot what is (according to N.Wells) wrong in this:
Quote (N.Wells @ Nov. 17 2016,17:42)

How Science sums up the Prufer study:
http://www.sciencemag.org/news.......latives
       
Quote
When the Max Planck scientists compared the bonobo genome directly with that of chimps and humans, however, they found that a small bit of our DNA, about 1.6%, is shared with only the bonobo, but not chimpanzees. And we share about the same amount of our DNA with only chimps, but not bonobos. These differences suggest that the ancestral population of apes that gave rise to humans, chimps, and bonobos was quite large and diverse genetically—numbering about 27,000 breeding individuals. Once the ancestors of humans split from the ancestor of bonobos and chimps more than 4 million years ago, the common ancestor of bonobos and chimps retained this diversity until their population completely split into two groups 1 million years ago. The groups that evolved into bonobos, chimps, and humans all retained slightly different subsets of this ancestral population's diverse gene pool—and those differences now offer clues today to the size and range of diversity in that ancestral group.



--------------
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

   
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Nov. 18 2016,18:46   

Quote (GaryGaulin @ Nov. 18 2016,19:21)
Quote (Texas Teach @ Nov. 18 2016,05:42)
 
Quote (GaryGaulin @ Nov. 17 2016,22:46)
 
Quote (N.Wells @ Nov. 17 2016,19:58)
   
Quote
That's more like it. You do need much more than that simple illustration to show what went where.

That "simple" illustration (actually, it's not that simple) shows quite adequately why your initial assertions are wrong.  If it's that simple, how come you don't understand it?

You only helped prove my point that it's not as simple as you have been making it seem by making both chimp "cousins" who are neatly out on a branch of their own.

Gary, this is stuff we teach in school.  No one is hiding the information from you.  Try learning something before shooting your mouth off.

If you know so much then you should be able to spot what is (according to N.Wells) wrong in this:
 
Quote (N.Wells @ Nov. 17 2016,17:42)

How Science sums up the Prufer study:
http://www.sciencemag.org/news.......latives
       
Quote
When the Max Planck scientists compared the bonobo genome directly with that of chimps and humans, however, they found that a small bit of our DNA, about 1.6%, is shared with only the bonobo, but not chimpanzees. And we share about the same amount of our DNA with only chimps, but not bonobos. These differences suggest that the ancestral population of apes that gave rise to humans, chimps, and bonobos was quite large and diverse genetically—numbering about 27,000 breeding individuals. Once the ancestors of humans split from the ancestor of bonobos and chimps more than 4 million years ago, the common ancestor of bonobos and chimps retained this diversity until their population completely split into two groups 1 million years ago. The groups that evolved into bonobos, chimps, and humans all retained slightly different subsets of this ancestral population's diverse gene pool—and those differences now offer clues today to the size and range of diversity in that ancestral group.


That's pretty dishonest.

Gary, everyone here understands this better than you.  No one other than you is having any trouble with the concepts or the evidence.
You don't have to keep trying to prove it.
If you can't keep up, keep quiet.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Nov. 18 2016,20:30   

Quote (GaryGaulin @ Nov. 18 2016,18:21)
Quote (Texas Teach @ Nov. 18 2016,05:42)
 
Quote (GaryGaulin @ Nov. 17 2016,22:46)
 
Quote (N.Wells @ Nov. 17 2016,19:58)
   
Quote
That's more like it. You do need much more than that simple illustration to show what went where.

That "simple" illustration (actually, it's not that simple) shows quite adequately why your initial assertions are wrong.  If it's that simple, how come you don't understand it?

You only helped prove my point that it's not as simple as you have been making it seem by making both chimp "cousins" who are neatly out on a branch of their own.

Gary, this is stuff we teach in school.  No one is hiding the information from you.  Try learning something before shooting your mouth off.

If you know so much then you should be able to spot what is (according to N.Wells) wrong in this:
 
Quote (N.Wells @ Nov. 17 2016,17:42)

How Science sums up the Prufer study:
http://www.sciencemag.org/news.......latives
       
Quote
When the Max Planck scientists compared the bonobo genome directly with that of chimps and humans, however, they found that a small bit of our DNA, about 1.6%, is shared with only the bonobo, but not chimpanzees. And we share about the same amount of our DNA with only chimps, but not bonobos. These differences suggest that the ancestral population of apes that gave rise to humans, chimps, and bonobos was quite large and diverse genetically—numbering about 27,000 breeding individuals. Once the ancestors of humans split from the ancestor of bonobos and chimps more than 4 million years ago, the common ancestor of bonobos and chimps retained this diversity until their population completely split into two groups 1 million years ago. The groups that evolved into bonobos, chimps, and humans all retained slightly different subsets of this ancestral population's diverse gene pool—and those differences now offer clues today to the size and range of diversity in that ancestral group.


Nothing is wrong with the facts quoted.  They do however contradict several of your assertions.  Nonetheless, let's play - what inferences do you draw from that information?

  
GaryGaulin



Posts: 5385
Joined: Oct. 2012

(Permalink) Posted: Nov. 18 2016,21:08   

I ended up needing to explain more detail to a geneticist who responded to my request for help figuring out what I have. Latest is here:

www.reddit.com/r/genetics/comments/5cz7eh/my_chromosome_banding_software_found_that_humans/da625vq/

--------------
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

   
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Nov. 19 2016,05:03   

That's a non-responsive attempt to change the topic.

Incidentally, "chromosome banding" is a misleading term for what you are doing, because "chromosome banding" already has a completely different meaning that produces results that slightly and superficially look like your results, so you are likely to create confusion.  Google Giemsa chromosome banding (sometimes abbreviated to G-banding, with or without the hyphen) for details.  

Also, have you provided an explanation anywhere of exactly what you are showing in your figures and how to interpret them, or at least legends and captions?  That would be helpful.  You appear to be working in triplets rather than individual bases?  For instance, how do single and double base deletions or additions show up (i.e. changes from ABC-ABC-ABC into BCA-BCA- or DAB-CAB-CAB?  How about reversals?

Note that the the geneticist who responded said, "It doesn't look like Bonobos are overall more related to humans than chimps (roughly equally related seems to be consensus)." That is in line with what I said and contradicts what you have claimed.  His comment, "it looks like a coarse version of synteny analysis", is not a compliment.

I would think that Fourier analysis would be the wrong tool to use to refine matching - no one has ever identified periodicity, cyclicity, or "return to the starting point" in DNA sequences, which is what Fourier analysis is designed to identify and work with.

A lot of alignment tools are already available: see
http://molbiol-tools.ca/Alignme....nts.htm
BLAST at https://blast.ncbi.nlm.nih.gov/Blast.c....ign2seq
ClustalW2 at http://www.ebi.ac.uk/Tools......ustalw2
SMS at http://www.bioinformatics.org/sms2.......na.html

You are probably going to want local alignment algorithms - see https://en.wikipedia.org/wiki.......ignment

  
Texas Teach



Posts: 2084
Joined: April 2007

(Permalink) Posted: Nov. 19 2016,11:31   

Quote (GaryGaulin @ Nov. 18 2016,18:21)
Quote (Texas Teach @ Nov. 18 2016,05:42)
 
Quote (GaryGaulin @ Nov. 17 2016,22:46)
 
Quote (N.Wells @ Nov. 17 2016,19:58)
   
Quote
That's more like it. You do need much more than that simple illustration to show what went where.

That "simple" illustration (actually, it's not that simple) shows quite adequately why your initial assertions are wrong.  If it's that simple, how come you don't understand it?

You only helped prove my point that it's not as simple as you have been making it seem by making both chimp "cousins" who are neatly out on a branch of their own.

Gary, this is stuff we teach in school.  No one is hiding the information from you.  Try learning something before shooting your mouth off.

If you know so much then you should be able to spot what is (according to N.Wells) wrong in this:
 
Quote (N.Wells @ Nov. 17 2016,17:42)

How Science sums up the Prufer study:
http://www.sciencemag.org/news.......latives
       
Quote
When the Max Planck scientists compared the bonobo genome directly with that of chimps and humans, however, they found that a small bit of our DNA, about 1.6%, is shared with only the bonobo, but not chimpanzees. And we share about the same amount of our DNA with only chimps, but not bonobos. These differences suggest that the ancestral population of apes that gave rise to humans, chimps, and bonobos was quite large and diverse genetically—numbering about 27,000 breeding individuals. Once the ancestors of humans split from the ancestor of bonobos and chimps more than 4 million years ago, the common ancestor of bonobos and chimps retained this diversity until their population completely split into two groups 1 million years ago. The groups that evolved into bonobos, chimps, and humans all retained slightly different subsets of this ancestral population's diverse gene pool—and those differences now offer clues today to the size and range of diversity in that ancestral group.


What I spot is someone who needs to approach learning with humility rather than arrogance.

Gary, imagine you have two first cousins who are brother and sister.  One is a similar height and has the same "family nose" as you.  The other shares your hair and eye color.

Which is more closely related to you?  Why?

--------------
"Creationists think everything Genesis says is true. I don't even think Phil Collins is a good drummer." --J. Carr

"I suspect that the English grammar books where you live are outdated" --G. Gaulin

  
ChemiCat



Posts: 532
Joined: Nov. 2013

(Permalink) Posted: Nov. 19 2016,14:38   

Quote
I ended up needing to explain more detail to a geneticist who responded to my request for help figuring out what I have.


It has been obvious for years that what you have is a big fat zero.

You are now totally misunderstanding "chromosome banding" along with "chemical species", along with "modelling" and along with "cognition".

By reading and researching the information and links provided by NoName and N.Wells you could save yourself a lot of embarrassment. By getting some high school science textbooks you could get a grounding in sciences. Instead you change the subject, spew invective and dig yourself an even deeper hole.

I certainly don't have the patience that NoName and N.Wells have in correcting the errors in your bullshit.

  
GaryGaulin



Posts: 5385
Joined: Oct. 2012

(Permalink) Posted: Nov. 19 2016,17:02   

Quote (N.Wells @ Nov. 19 2016,05:03)
I would think that Fourier analysis would be the wrong tool to use to refine matching - no one has ever identified periodicity, cyclicity, or "return to the starting point" in DNA sequences, which is what Fourier analysis is designed to identify and work with.

There is no doubt that other methods are sometimes useful. In this case though what is to be aligned starts off as a simple gray scale that is already reduced down to rows of readings less than 1000 pixels wide. Any one of the rows contains an ideal waveform to use for Fourier analysis.

--------------
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

   
NoName



Posts: 2729
Joined: Mar. 2013

(Permalink) Posted: Nov. 19 2016,17:28   

Quote (GaryGaulin @ Nov. 19 2016,18:02)
Quote (N.Wells @ Nov. 19 2016,05:03)
I would think that Fourier analysis would be the wrong tool to use to refine matching - no one has ever identified periodicity, cyclicity, or "return to the starting point" in DNA sequences, which is what Fourier analysis is designed to identify and work with.

There is no doubt that other methods are sometimes useful. In this case though what is to be aligned starts off as a simple gray scale that is already reduced down to rows of readings less than 1000 pixels wide. Any one of the rows contains an ideal waveform to use for Fourier analysis.

You really have no clue whatsoever about the difference between a map and the territory mapped, do you?
"Pixel" is not a unit of measurement that applies to genes or chromosomes.  Not even by analogy.
You can 'align images' all day and all night and not learn a thing about the object being imaged.

"Pixels"
Good fucking god you're stupid.

  
GaryGaulin



Posts: 5385
Joined: Oct. 2012

(Permalink) Posted: Nov. 19 2016,19:56   

Quote (N.Wells @ Nov. 19 2016,05:03)
Also, have you provided an explanation anywhere of exactly what you are showing in your figures and how to interpret them, or at least legends and captions?  That would be helpful.


I added a ReadMe file to the DIGITAL banding software, where nothing has to get wet and you don't need an expensive microscope to see the results. I'm also adding more information to program comments, I will later extract for another ReadMe for the main folder with the program in it. Some of what I wrote to an experienced geneticist at the genetics forum can be included. In comparison to the navigation network project it's a quick one to get ready for Planet Source Code and maybe the online journal Bob O'H much earlier on in this thread mentioned.

   
Quote
This folder named "DNA" contains subfolders (each a different ChromoType) for downloaded Fasta format DNA files. The first two letters of a folder's name is by the program used for two letter names such as "Hu" or "Go" that are used in the illustration. An underscore in the folder name omits all else after (used to indicate which assembly the data contains) from the fully spelled out "Human" or "Gorilla" type name.

Fasta files are too large to include with the program but can be downloaded from:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/

The very first genome assemblies had blocks of missing information that the reading method could not get a read on. Over time most of the missing information became included. But there are still unread areas that have a "N" instead of A,C,G,T. It's convenient to include enough of the assembly related information to know whether any on the list can be updated.

The reference assembly you want for human should end with "chr2.fa.gz". For example "hs_ref_GRCh38.p7_chr2.fa.gz" For others you need "chr2A.fa.gz" and the "chr2B.fa.gz" files.

Human:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/CHR_02/

Bonobo:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pan_paniscus/CHR_2A/
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pan_paniscus/CHR_2B/

Common Chimp:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pan_troglodytes/CHR_2A/
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pan_troglodytes/CHR_2B/

Gorilla:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Gorilla_gorilla/CHR_2A/
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Gorilla_gorilla/CHR_2B/

Orangutan:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pongo_abelii/CHR_2A/
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pongo_abelii/CHR_2B/

After unzipping the chromosome to a ".fa" file then starting program its name will appear in the "Fasta files" listbox. Clicking on it will compile the data to what the program uses for extracting information from it. It's then all set to use in a comparison, by clicking on it and the other ChromoTypes you want to compare then "Create Illustration" to assemble the information into illustrations that are saved to the BitMaps folder.

You can type in your name to include in the credits that get written into the illustration. I am not able to regularly compile new ones, but was able to write the software that makes it possible for you to do so. Have fun, enjoy.

Gary


--------------
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

   
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Nov. 19 2016,20:43   

Quote (GaryGaulin @ Nov. 19 2016,19:56)
Quote (N.Wells @ Nov. 19 2016,05:03)
Also, have you provided an explanation anywhere of exactly what you are showing in your figures and how to interpret them, or at least legends and captions?  That would be helpful.


I added a ReadMe file to the DIGITAL banding software, where nothing has to get wet and you don't need an expensive microscope to see the results. I'm also adding more information to program comments, I will later extract for another ReadMe for the main folder with the program in it. Some of what I wrote to an experienced geneticist at the genetics forum can be included. In comparison to the navigation network project it's a quick one to get ready for Planet Source Code and maybe the online journal Bob O'H much earlier on in this thread mentioned.

   
Quote
This folder named "DNA" contains subfolders (each a different ChromoType) for downloaded Fasta format DNA files. The first two letters of a folder's name is by the program used for two letter names such as "Hu" or "Go" that are used in the illustration. An underscore in the folder name omits all else after (used to indicate which assembly the data contains) from the fully spelled out "Human" or "Gorilla" type name.

Fasta files are too large to include with the program but can be downloaded from:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/

The very first genome assemblies had blocks of missing information that the reading method could not get a read on. Over time most of the missing information became included. But there are still unread areas that have a "N" instead of A,C,G,T. It's convenient to include enough of the assembly related information to know whether any on the list can be updated.

The reference assembly you want for human should end with "chr2.fa.gz". For example "hs_ref_GRCh38.p7_chr2.fa.gz" For others you need "chr2A.fa.gz" and the "chr2B.fa.gz" files.

Human:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/CHR_02/

Bonobo:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pan_paniscus/CHR_2A/
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pan_paniscus/CHR_2B/

Common Chimp:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pan_troglodytes/CHR_2A/
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pan_troglodytes/CHR_2B/

Gorilla:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Gorilla_gorilla/CHR_2A/
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Gorilla_gorilla/CHR_2B/

Orangutan:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pongo_abelii/CHR_2A/
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pongo_abelii/CHR_2B/

After unzipping the chromosome to a ".fa" file then starting program its name will appear in the "Fasta files" listbox. Clicking on it will compile the data to what the program uses for extracting information from it. It's then all set to use in a comparison, by clicking on it and the other ChromoTypes you want to compare then "Create Illustration" to assemble the information into illustrations that are saved to the BitMaps folder.

You can type in your name to include in the credits that get written into the illustration. I am not able to regularly compile new ones, but was able to write the software that makes it possible for you to do so. Have fun, enjoy.

Gary

Thanks, but if your quote is your explanation, then that is not what I meant.  How you are processing and displaying the data remains opaque.  What's your reasoning behind whatever you are doing to the data?  What do you mean by "to band chromosomes according to the abundance of all the three letter codon possibilities that exist. In a way like counting from AAA to TTT, none get left out. Reverse complements are shown in the same band so that slight variations in predicted equal content can be seen and this way shows 64 possibilities in 32 comparisons."

I have very little idea of what I am looking at in https://sites.google.com/site....20.png, for example, how to read the information that you are presenting.

  
GaryGaulin



Posts: 5385
Joined: Oct. 2012

(Permalink) Posted: Nov. 19 2016,22:11   

Quote (N.Wells @ Nov. 19 2016,20:43)
Quote (GaryGaulin @ Nov. 19 2016,19:56)
Quote (N.Wells @ Nov. 19 2016,05:03)
Also, have you provided an explanation anywhere of exactly what you are showing in your figures and how to interpret them, or at least legends and captions?  That would be helpful.


I added a ReadMe file to the DIGITAL banding software, where nothing has to get wet and you don't need an expensive microscope to see the results. I'm also adding more information to program comments, I will later extract for another ReadMe for the main folder with the program in it. Some of what I wrote to an experienced geneticist at the genetics forum can be included. In comparison to the navigation network project it's a quick one to get ready for Planet Source Code and maybe the online journal Bob O'H much earlier on in this thread mentioned.

     
Quote
This folder named "DNA" contains subfolders (each a different ChromoType) for downloaded Fasta format DNA files. The first two letters of a folder's name is by the program used for two letter names such as "Hu" or "Go" that are used in the illustration. An underscore in the folder name omits all else after (used to indicate which assembly the data contains) from the fully spelled out "Human" or "Gorilla" type name.

Fasta files are too large to include with the program but can be downloaded from:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/

The very first genome assemblies had blocks of missing information that the reading method could not get a read on. Over time most of the missing information became included. But there are still unread areas that have a "N" instead of A,C,G,T. It's convenient to include enough of the assembly related information to know whether any on the list can be updated.

The reference assembly you want for human should end with "chr2.fa.gz". For example "hs_ref_GRCh38.p7_chr2.fa.gz" For others you need "chr2A.fa.gz" and the "chr2B.fa.gz" files.

Human:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/CHR_02/

Bonobo:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pan_paniscus/CHR_2A/
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pan_paniscus/CHR_2B/

Common Chimp:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pan_troglodytes/CHR_2A/
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pan_troglodytes/CHR_2B/

Gorilla:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Gorilla_gorilla/CHR_2A/
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Gorilla_gorilla/CHR_2B/

Orangutan:
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pongo_abelii/CHR_2A/
'ftp://ftp.ncbi.nlm.nih.gov/genomes/Pongo_abelii/CHR_2B/

After unzipping the chromosome to a ".fa" file then starting program its name will appear in the "Fasta files" listbox. Clicking on it will compile the data to what the program uses for extracting information from it. It's then all set to use in a comparison, by clicking on it and the other ChromoTypes you want to compare then "Create Illustration" to assemble the information into illustrations that are saved to the BitMaps folder.

You can type in your name to include in the credits that get written into the illustration. I am not able to regularly compile new ones, but was able to write the software that makes it possible for you to do so. Have fun, enjoy.

Gary

Thanks, but if your quote is your explanation, then that is not what I meant.  How you are processing and displaying the data remains opaque.  What's your reasoning behind whatever you are doing to the data?  What do you mean by "to band chromosomes according to the abundance of all the three letter codon possibilities that exist. In a way like counting from AAA to TTT, none get left out. Reverse complements are shown in the same band so that slight variations in predicted equal content can be seen and this way shows 64 possibilities in 32 comparisons."

I have very little idea of what I am looking at in https://sites.google.com/site.......20.png, for example, how to read the information that you are presenting.

Your link has a tiny poop at the end. This works:

sites.google.com/site/digitalchromosomebanding/home/TripletAbundanceOrangutanGorillaChimpBonoboHumanChr2Brightness20.png

To help understand how it works I'm considering using an algorithm that uses the hard drive to sort out 3,4,5 and more length strings. After three the detail becomes more specific in regards to function. At 3 there is an excellent overall view, but it's not expected to show the detail that should come from going past that string length.

This generates Fourier compatible markers galore to use for sorting out what came from where. Whether it is a gene or not then does not matter.

--------------
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

   
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Nov. 19 2016,22:36   

Quote
To help understand how it works I'm considering using an algorithm that uses the hard drive to sort out 3,4,5 and more length strings. After three the detail becomes more specific in regards to function. At 3 there is an excellent overall view, but it's not expected to show the detail that should come from going past that string length.

This generates Fourier compatible markers galore to use for sorting out what came from where. Whether it is a gene or not then does not matter.

That still doesn't help.  It doesn't matter whether you are using the hard drive or not.  By "sort out" I assume you mean "identify", or do you mean something else.  Are you starting strings at the end of each previous string (i.e., no overlaps), or at each base in the chain (i.e., lots of overlaps, but it doesn't matter if a set has become offset by one or two bases).  Since codons are sets of 3, how does going beyond three become more specific in terms of function (unless you are referring simply to entire proteins and their functions?).  It remains unclear how to interpret your diagram.

  
GaryGaulin



Posts: 5385
Joined: Oct. 2012

(Permalink) Posted: Nov. 19 2016,23:13   

Quote (N.Wells @ Nov. 19 2016,22:36)
Quote
To help understand how it works I'm considering using an algorithm that uses the hard drive to sort out 3,4,5 and more length strings. After three the detail becomes more specific in regards to function. At 3 there is an excellent overall view, but it's not expected to show the detail that should come from going past that string length.

This generates Fourier compatible markers galore to use for sorting out what came from where. Whether it is a gene or not then does not matter.

That still doesn't help.  It doesn't matter whether you are using the hard drive or not.  By "sort out" I assume you mean "identify", or do you mean something else.  Are you starting strings at the end of each previous string (i.e., no overlaps), or at each base in the chain (i.e., lots of overlaps, but it doesn't matter if a set has become offset by one or two bases).  Since codons are sets of 3, how does going beyond three become more specific in terms of function (unless you are referring simply to entire proteins and their functions?).  It remains unclear how to interpret your diagram.

The program takes the Fasta file one (A,C,G,T) base location at a time, while counting how many of each of the possible three letter codons there are in each given horizontal band lines along the chromosome.

--------------
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

   
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Nov. 20 2016,03:04   

Progress of a sort, thank you.
What do you mean by "each horizontal band line along the chromosome"?
Why do you want each possible triplet?  Alternative splicing happens, but not every possible triple gets used, and indeed much of the chromosome goes entirely uncoded.
Once you have that data, how does your program display it?

  
GaryGaulin



Posts: 5385
Joined: Oct. 2012

(Permalink) Posted: Nov. 20 2016,18:19   

Quote (N.Wells @ Nov. 20 2016,03:04)
Progress of a sort, thank you.
What do you mean by "each horizontal band line along the chromosome"?
Why do you want each possible triplet?  Alternative splicing happens, but not every possible triple gets used, and indeed much of the chromosome goes entirely uncoded.
Once you have that data, how does your program display it?

More info:

Quote
This program digitally bands chromosomes according to the abundance of (4^3) 64 possible three letter DNA sequences:

AAA,AAC,AAG,AAT,
ACA,ACC,ACG,ACT,
AGA,AGC,AGG,AGT,
ATA,ATC,ATG,ATT,
CAA,CAC,CAG,CAT,
CCA,CCC,CCG,CCT,
CGA,CGC,CGG,CGT,
CTA,CTC,CTG,CTT,
GAA,GAC,GAG,GAT,
GCA,GCC,GCG,GCT,
GGA,GGC,GGG,GGT,
GTA,GTC,GTG,GTT,
TAA,TAC,TAG,TAT,
TCA,TCC,TCG,TCT,
TGA,TGC,TGG,TGT,
TTA,TTC,TTG,TTT

For each selected Assembly (such as Human_, Bonobo_) found in the DNA folder: the program scans through Fasta format files one (A,C,G,T) base location at a time, while counting how many times each of the 64 triplets occur in each of the one pixel wide vertical band lines shown along the horizontal length of the chromosome. A "Bases per Band" scrollbar controls how many base pairs each band line represents.

A "Brightness" control is provided for adjusting how brightly the abundances are displayed in the illustration. To better show banding of low abundance sequences there is an optional "Brightness Adjust" checkbox for making each of the 32 horizontal groups the same brightness, regardless of overall abundances.

When comparing with our closest descendents our fused Chromosome 2 has a corresponding part A that is shown in the above left, while part B is shown below right of the fused chromosome.


The method used to find the strings is very fast but only works for a string length of 3 and is not easy to figure out, and work with. There is already a step where it scans through the entire fasta file anyway and it would seem to simplify things by taking the chromosome one pixel worth of bases (instead of line of pixels all the same color) at a time then show folded up with an up and down accordion fold, or in fragments all going the same way. The "bands" will then also have a signature texture.

--------------
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

   
jeffox



Posts: 671
Joined: Oct. 2007

(Permalink) Posted: Nov. 21 2016,11:35   

Quote
The "bands" will then also have a signature texture.


You mean they'll look like John Hancock?!??

:)  :)  :)  

Whatta hoot!!!!!!!!!!!

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Nov. 22 2016,07:12   

Why do you think that working with all possible triplets is better than just working with the sequences taken one nucleotide at a time?

  
NoName



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Joined: Mar. 2013

(Permalink) Posted: Nov. 22 2016,08:52   

What do you think this work has to do with your "theory"?

What do you think this work has to do with your software?

  
GaryGaulin



Posts: 5385
Joined: Oct. 2012

(Permalink) Posted: Nov. 22 2016,15:27   

Quote (NoName @ Nov. 22 2016,08:52)
What do you think this work has to do with your "theory"?

Chromosomal Adam and Eve.

Quote (NoName @ Nov. 22 2016,08:52)
What do you think this work has to do with your software?

Helps figure out how to use the algorithm used in the ID Lab to model the developmental behavior of complex genetic systems.

--------------
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

   
GaryGaulin



Posts: 5385
Joined: Oct. 2012

(Permalink) Posted: Nov. 22 2016,16:13   

Quote (N.Wells @ Nov. 22 2016,07:12)
Why do you think that working with all possible triplets is better than just working with the sequences taken one nucleotide at a time?

The banding method was in part inspired by Guenter's info. This is from program comments:

 
Quote

From:  http://www.basic.northwestern.edu/g-buehler/genomes/genome.htm

The universal Codon spectrum (majorityn distribution)- also the work of countless inversions and inverted transpositions.
The infinity of conceivable Codon distributions.
Chargaff's second parity rule specifies only that the numbers of Codons are equal to the numbers of their reverse complements
in every sufficiently long genomic DNA strand. But it does not specify the numbers of each Codon.
In fact, there is an infinity of possible Codon distributions, that all fulfill the rule and, yet, are all different from each other.
This is easy to show. There are 64 different [three letter] Codons.
They can be divided into 2 groups where the members of one group are the reverse complements of the members of the other.
For example, one such division could consist of the following groups.
GROUP 1: AGT, ATT, CAT, CCT, CGG, CGT, CTG, CTT, GAA, GAG, GAT, GCA, GCG, GCT, GGA, GGC, GGG, GGT, GTA, GTC, GTG, GTT, TAG, TAT, TCG, TCT, TGA, TGG, TGT, TTA, TTG, TTT.
GROUP 2: ACT, AAT, ATG, AGG, CCG, ACG, CAG, AAG, TTC, CTC, ATC, TGC, CGC, AGC, TCC, GCC, CCC, ACC, TAC, GAC, CAC, AAC, CTA, ATA, CGA, AGA, TCA, CCA, ACA, TAA, CAA, AAA

-----------

The illustration banding pattern shows both the GROUP 1 and GROUP 2 abundances.
On the very left you will see the corresponding three letter "AGT, ATT, CAT,," pair being shown in that row.
Their unusual closeness made it possible to show 64 triplet possibilities in only 32 comparisons.


After finding out how well this works for mathematically dissecting chromosomes the next logical step became to use the same idea for other sequence lengths. The program started with three, but all other lengths of unique coding are now needed. How that all together branches out helps show the systematics of the system needing to be modeled.

--------------
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

   
GaryGaulin



Posts: 5385
Joined: Oct. 2012

(Permalink) Posted: Nov. 22 2016,16:37   

Quote (jeffox @ Nov. 21 2016,11:35)
Quote
The "bands" will then also have a signature texture.


You mean they'll look like John Hancock?!??

:)  :)  :)  

Whatta hoot!!!!!!!!!!!

Sort of, yes. At this level too: features of living things are easily recognized by their signature uniquenesses. I give a hoot about that.

--------------
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

   
jeffox



Posts: 671
Joined: Oct. 2007

(Permalink) Posted: Nov. 22 2016,18:37   

Signature differences?  You mean like between the red and yellow varieties of A. Muscaria?  :)

Just thought I'd ask . . . .

Whatta hoot!!!!!

:)  :)  :)  :)   :)

  
jeffox



Posts: 671
Joined: Oct. 2007

(Permalink) Posted: Nov. 22 2016,18:41   

Signature uniquenesses*.  My bad.

  
N.Wells



Posts: 1836
Joined: Oct. 2005

(Permalink) Posted: Nov. 22 2016,18:52   

Quote (GaryGaulin @ Nov. 22 2016,16:13)
Quote (N.Wells @ Nov. 22 2016,07:12)
Why do you think that working with all possible triplets is better than just working with the sequences taken one nucleotide at a time?

The banding method was in part inspired by Guenter's info. This is from program comments:

   
Quote

From:  http://www.basic.northwestern.edu/g-buehler/genomes/genome.htm

The universal Codon spectrum (majorityn distribution)- also the work of countless inversions and inverted transpositions.
The infinity of conceivable Codon distributions.
Chargaff's second parity rule specifies only that the numbers of Codons are equal to the numbers of their reverse complements
in every sufficiently long genomic DNA strand. But it does not specify the numbers of each Codon.
In fact, there is an infinity of possible Codon distributions, that all fulfill the rule and, yet, are all different from each other.
This is easy to show. There are 64 different [three letter] Codons.
They can be divided into 2 groups where the members of one group are the reverse complements of the members of the other.
For example, one such division could consist of the following groups.
GROUP 1: AGT, ATT, CAT, CCT, CGG, CGT, CTG, CTT, GAA, GAG, GAT, GCA, GCG, GCT, GGA, GGC, GGG, GGT, GTA, GTC, GTG, GTT, TAG, TAT, TCG, TCT, TGA, TGG, TGT, TTA, TTG, TTT.
GROUP 2: ACT, AAT, ATG, AGG, CCG, ACG, CAG, AAG, TTC, CTC, ATC, TGC, CGC, AGC, TCC, GCC, CCC, ACC, TAC, GAC, CAC, AAC, CTA, ATA, CGA, AGA, TCA, CCA, ACA, TAA, CAA, AAA

-----------

The illustration banding pattern shows both the GROUP 1 and GROUP 2 abundances.
On the very left you will see the corresponding three letter "AGT, ATT, CAT,," pair being shown in that row.
Their unusual closeness made it possible to show 64 triplet possibilities in only 32 comparisons.


After finding out how well this works for mathematically dissecting chromosomes the next logical step became to use the same idea for other sequence lengths. The program started with three, but all other lengths of unique coding are now needed. How that all together branches out helps show the systematics of the system needing to be modeled.

I'm thinking that if you can work in the Time Cube, you might really have something.  Unique, that is.

  
GaryGaulin



Posts: 5385
Joined: Oct. 2012

(Permalink) Posted: Nov. 22 2016,19:27   

Quote (jeffox @ Nov. 22 2016,18:41)
Signature uniquenesses*.  My bad.

I was attempting to creative relate the normally boring scientific concept of "chemical signatures" to the "unique address" of computer RAM chip data.

--------------
The theory of intelligent design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection.

   
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