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Old 01-22-2015, 01:34 PM   #1
Dave_Carlson
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Default Converting Blast+ output to Fasta sequence files

Hi All,

I have a bioinformatics problem that I'm hoping others have encountered (and solved) already.

I have a transcriptome that I have BLASTed against itself to look for putatively-paralogous genes. Right now the Blastn results are in tab-separated format, with several thousand rows of results. After filtering the results to remove unhelpful stuff (e.g., very, very short hsp's or sequences that hit to themselves), what I would like to be able to do is take each hit between two sequences, find the full sequences in the original transcriptome fasta file and output the two sequences into a new fasta file. Ideally, I would like to able to do this in a relatively automated manner, so that I get separate fasta files for each hit from my Blastn results.

Is anybody aware of a script or utility that could do something like that? My coding skills are not great, and I'm hoping that I don't have to spend a lot of time inventing (reinventing?) the wheel on this. Any help or suggestions would be appreciated! Thanks.
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Old 01-22-2015, 07:28 PM   #2
maubp
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You probably want to use blastdbcmd to pull the full sequences from the BLAST database (assuming you are using NCBI BLAST+, this tool had a different name in NCBI legacy BLAST).
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Old 01-23-2015, 08:51 AM   #3
Dave_Carlson
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Quote:
Originally Posted by maubp View Post
You probably want to use blastdbcmd to pull the full sequences from the BLAST database (assuming you are using NCBI BLAST+, this tool had a different name in NCBI legacy BLAST).
Thanks for the suggestion! Based on other threads I've seen, I had been considering using blastdbcmd, however if I understand correctly, this will only output a single file containing whatever sequences correspond to the ID's from the list provided as an argument. Is there a way to make blastdbcmd output multiple files?
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Old 01-23-2015, 01:22 PM   #4
maubp
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If you want one sequence per FASTA file, either call blastdbcmd many times in a loop, or divide the big FASTA file using a tool like EMBOSS seqretsplit http://emboss.open-bio.org/rel/rel6/...qretsplit.html or a simple script.
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Old 01-23-2015, 09:05 PM   #5
Dave_Carlson
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Quote:
Originally Posted by maubp View Post
If you want one sequence per FASTA file, either call blastdbcmd many times in a loop, or divide the big FASTA file using a tool like EMBOSS seqretsplit http://emboss.open-bio.org/rel/rel6/...qretsplit.html or a simple script.
Thanks! With a bit of fiddling around, I was able to get blastdbcmd to output the sequences I needed (and in the order I needed them to be in), and then I used Fasta Splitter to separate the putatively-paralogous sequences into their own files. Thanks for taking the time to help me!
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Old 01-25-2015, 03:27 AM   #6
maubp
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Good work
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