Moderator: a.zielezinski

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a.zielezinski6.9k
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Andrzej Zielezinski

Posts by a.zielezinski

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Comment: C: NCBI vs Ensembl - which one to chose - for downloading protein fasta files
... Uniprot has built a database of reference proteomes for most organisms sequences today: http://www.uniprot.org/proteomes/ ...
written 1 hour ago by a.zielezinski6.9k
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Answer: A: why only 2 amino acids are used in gene prediction
... Hexamers (6 nt long words) are accepted as the most accurate *k*-mer frequency based measure of coding potential. In 1992, a systematic study of more than twenty compositional properties indicated that hexamer composition gave the best discrimination between coding and non-coding regions ([Fickett & ...
written 2 hours ago by a.zielezinski6.9k
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Comment: C: OrthoMCL step 12: [mclxReadDimensions] could not parse header
... If Philipp and lu.ne correctly answered your question, please accept their answers by clicking on the check mark beside their posts. Accepting an answer is important as it both rewards posters for solving your problem and informs others that your issue is resolved. If an answer has helped you solve ...
written 4 days ago by a.zielezinski6.9k
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Answer: A: Bacterial phylogeny download for a list of species
... [NCBI Taxonomy database][1] provides a feature named [Common Tree][2], where you can provide a list of taxonomy identifiers to create a tree of species you are interested in. The tree will be displayed in your browser and you can save it to a file (in text or Newick format). For example, here is a ...
written 6 days ago by a.zielezinski6.9k
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Answer: A: [BioPython] Parse blast tabular output
... A long time ago I wrote a module for handling tabular BLAST output (`-outfmt 6` / `-m8`). Maybe you will find it useful. \gist https://gist.github.com/aziele/e060d1c0d1ef2acb4bd67e2fc0f165a6 **SAMPLE USAGE:** Filename: `test.outfmt6` cgl|CAGL0A00187g ecy|Ecym_8168 31.11 90 49 3 597 676 95 18 ...
written 6 days ago by a.zielezinski6.9k
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Comment: C: genomics overlap python error
... Sorry for that, I made a mistake. It should be: `st, en = [cst, cen] if cstr == '+' else [cen, cst]`. I also corrected the answer. If you want start always less than end (regardless of the strand), just change this line to `st, en = cst, cen`. ...
written 10 days ago by a.zielezinski6.9k
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Comment: C: InParanoid ERROR : "Blast output file A->B is missing", No sqltable output file
... How about duplicated identifiers (e.g. OCTO)? ...
written 11 days ago by a.zielezinski6.9k
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Comment: C: InParanoid ERROR : "Blast output file A->B is missing", No sqltable output file
... I had the same error once. If I remember well, this had something to do with FASTA definition lines. In my case, InParanoid didn't parse FASTA sequences correctly if they contained quote characters etc. Check your query files - it would be best if you limit the FASTA definition lines to identifier o ...
written 12 days ago by a.zielezinski6.9k
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Comment: C: genomics overlap python error
... To write the output to a file, just run the script and redirect the output to a file (`python script.py > output.txt`). To combine cases where a coordinate maps to multiple genes use something like this: d = {} fh = open('output.txt') for line in fh: sl = line.split() ...
written 14 days ago by a.zielezinski6.9k
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Comment: C: genomics overlap python error
... Since the script already reports cases where a coordinate maps to multiple genes, the easiest way to get to your desired output would be to write another script that would reformat existing output. ...
written 14 days ago by a.zielezinski6.9k

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