How to Extract Multiple Sequence from Multi Fasta File by ID list

Anti · 02-02-2015, 01:58 AM

Hi,
I have a list of ids in .txt format and a multi fasta file with sequences. I need to extract sequences with the IDs in the list.

Can you help me, please?

mike.t · 02-02-2015, 03:16 AM

I think you can do that using seqret which is part of EMBOSS. According to the documentation the paramater -iquery1 can be used to specify a list of IDs, although probably not a file with IDs...

maubp · 02-02-2015, 04:46 AM

Do you program? You can do that with a few lines using a library like Biopython.

Alternatively, if you have a local Galaxy you could ask your admin to install one of these tools: http://toolshed.g2.bx.psu.edu/view/p...q_filter_by_id or http://toolshed.g2.bx.psu.edu/view/p...q_select_by_id

rhinoceros · 02-02-2015, 04:55 AM

If there are no linebreaks in the sequences, then

Code:

grep -A1 -w -f id.txt seqFile.fasta > output.fasta

should work. The ids have to be identical to the fasta headers including the greater than sign.

GenoMax · 02-02-2015, 05:02 AM

faSomeRecords from Kent utilities is the simplest solution (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/)

More here: http://seqanswers.com/forums/showpos...0&postcount=13

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02-02-2015, 01:58 AM	#1
Anti Junior Member Location: Italy Join Date: Sep 2014 Posts: 5	How to Extract Multiple Sequence from Multi Fasta File by ID list Hi, I have a list of ids in .txt format and a multi fasta file with sequences. I need to extract sequences with the IDs in the list. Can you help me, please?

02-02-2015, 04:55 AM	#4
rhinoceros Senior Member Location: sub-surface moon base Join Date: Apr 2013 Posts: 372	If there are no linebreaks in the sequences, then Code: grep -A1 -w -f id.txt seqFile.fasta > output.fasta should work. The ids have to be identical to the fasta headers including the greater than sign. __________________ savetherhino.org

02-02-2015, 03:16 AM	#2
mike.t Member Location: Spain Join Date: Mar 2010 Posts: 36	I think you can do that using seqret which is part of EMBOSS. According to the documentation the paramater -iquery1 can be used to specify a list of IDs, although probably not a file with IDs...

02-02-2015, 04:46 AM	#3
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	Do you program? You can do that with a few lines using a library like Biopython. Alternatively, if you have a local Galaxy you could ask your admin to install one of these tools: http://toolshed.g2.bx.psu.edu/view/p...q_filter_by_id or http://toolshed.g2.bx.psu.edu/view/p...q_select_by_id

02-02-2015, 05:02 AM	#5
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,091	faSomeRecords from Kent utilities is the simplest solution (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/) More here: http://seqanswers.com/forums/showpos...0&postcount=13