This is a test version of Biostars. For the public version, visit https://www.biostars.org.
How can i find longest sequence in fasta file on terminal

I have protein file in fasta format and I want to find the longest sequence. What should I do? The codes I found did not solve my problem, as they included the nomenclature in the length.

fasta sequence
• 3,811 views • link
updated by Ram Ram • written by logbio • logbio

Thank you for answer but your code is not solve my problem :/

• 0 views • link
written by logbio • logbio

so, show us what you tried, and what failed and why.

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

I thought I included the code but I'm unpublished, sorry.

The fasta file I have is as follows

>NP_000005.3 alpha-2-macroglobulin isoform a precursor [Homo sapiens] MGKNKLLHPSLVLLLLVLLPTDAS....
>NP_000010.1 acetyl-CoA acetyltransferase, mitochondrial isoform b precursor [Homo sapiens] MAVLAALLRSGARSRSPLLRLVQEI... . . .

I want to find the longest sequence in this file excluding naming. However, when I run the code you have given, it does not give an error and does not give any output.

• 0 views • link
written by logbio • logbio

the code(s) was/were an inspiration. You should understand it and adapt it to your needs.

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

1 answer

Here is one option using GNU tools only:

grep -v '>' seq.fasta | awk '{print $0"\t"length($0)}' | sort -n -k2 -r
• 0 views • link
written by liorglic liorglic

Your code is work but not gives sequence properties. (ID etc)

• 0 views • link
written by logbio • logbio

Well, you need to specify what you want your output to look like. In general, if you want better control then I suggest you look into bioawk or biopython SeqIO.

• 0 views • link
written by liorglic liorglic

Log in to answer this question.

More posts like this