GaryGaulin
Posts: 5385
Joined: Oct. 2012
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| 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 |
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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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