User: zgayk

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zgayk90
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United States
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4 years, 8 months ago
Joined:
5 years, 9 months ago
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Posts by zgayk

<prev • 38 results • page 1 of 4 • next >
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Comment: C: Sorting BLAST output files together?
... I am familiar with biopython, but have not used it for this task. Could you recommend a particular biopython function for this? Thanks, Zach ...
written 4.7 years ago by zgayk90
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Comment: C: Sorting BLAST output files together?
... I outputted the blast results in output format 7, the one that gives the actual sequences of both subject and match. The sort worked, butI'm just not sure how to modify it to line up the sequences for each gene so I can extract the sequences for each species and then align the sequences. ...
written 4.7 years ago by zgayk90
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Comment: C: Sorting BLAST output files together?
... This is all I have done so far and it sorted all the sequences from the same species together, so I need to figure how to modify sort to sort by gene first, and then species. Not sure how to deal with the problem of genes missing in one genome, but present in the others. cat outputExpandedPA.blast. ...
written 4.7 years ago by zgayk90
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Comment: C: Sorting BLAST output files together?
... What I'm not sure is if a gene is missing from one of the blast files, but present in the other four, wouldn't the genes not all line up across all five species? I have not actually used cat and sort, but have been reading that this might work. Would you have any ideas of a possible script? ...
written 4.7 years ago by zgayk90
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Sorting BLAST output files together?
... Hi, I have five BLASTn tabular files that resulted from querying the same large gene list (same query) against a different subject genome database for each resulting file. The goal was to potentially identify possible orthologous sequences between the subject gene list and the 5 different match gen ...
blast written 4.7 years ago by zgayk90
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Comment: C: BLAST Multiple Subject sequences?
... Thank you very much for your help. The reciprocal best hits approach sounds like something to use in the future. RIght now I am just trying to get a cursory feel for what may be an orthologous gene using basic blastn, and later using a script to remove those that look like parlalogs. But, I will kee ...
written 4.7 years ago by zgayk90
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Comment: C: BLAST Multiple Subject sequences?
... Thanks very much for the ideas, and sorry about the late response. I have done what you suggested under 2) and now have five blast databases, one for each bird species. But now the question I am struggling with is how to parse all five databases, each with a single alignment to the query, so that I ...
written 4.7 years ago by zgayk90
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BLAST Multiple Subject sequences?
... I am trying to locate the orthologs of genes identified in a genome assembly in five other bird genomes (red-throated loon, adelie penguin, northern fulmar, chicken, pigeon). To do this I made a blast database of each of the five genomes: makeblastdb -in '"Columba_livia.cds" "Fulmarus_glacialis.c ...
blast written 4.9 years ago by zgayk90 • updated 4.9 years ago by pld4.9k
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Identifying frame of blast gene fragment
... Hi,    I want to compare a large list of fragments of gene sequences between two species using dN/dS. The problem is that some of these gene fragments might start with the last nucleotide of a codon rather than a whole codon and the program I am using to compute dN/dS will of course count the read ...
gene sequence blast written 5.3 years ago by zgayk90
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Comment: C: Missing Blast fields in outfmt 6
... Thank you, I figured out what was wrong. Blast wasn't reading all the fields becuase the code wasn't all on one line. ...
written 5.4 years ago by zgayk90

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