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Find sequences in a fast files present in another fasta file

Hi all

I have a fasta fileA.fasta which contains 15 sequences and another fasta fileB.fasta which contains 92 sequences. I would like to find how many of the 15 sequences are also found amongst the 92.

The format (for both files is the same) is like this:

>ENST000006553_1908 
AGCGGGGCCCTT

>ENST000002542_1826 
GGGCCTAAAATT

...and so on

sequence
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updated by Ram Ram • written by lorenzinip • lorenzinip

Do the sequences match exactly? Also, is there any match in the names?

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written by rpolicastro rpolicastro

2 answers

Exact sequence match, headers don't need to match, no linebreaks in sequences:

join -1 2 -2 2 -t $'\t' \
    <(paste -d $'\t' - - < f1.fasta | sort -t $'\t' -k2,2) \
    <(paste -d $'\t' - - < f2.fasta | sort -t $'\t' -k2,2)
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written by 5heikki 5heikki

with seqkit:

   $ seqkit common -si input1.fa input2.fa

order of the files doesn't matter.

Check if following awk script works:

$ awk -v RS=">" -v OFS="\n"  'NF > 1 && NR==FNR {a[$1,$2];next} ($1,$2) in a {print ">"$1,$2}' input1.fa input2.fa

if fasta file is flattened and sequence and IDs are identical in both the files, following awk script should work:

$ awk  'FNR==NR {a[$1]=$0; next}; $1 in a  {print $1}' input1.fa input2.fa
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written by cpad0112 cpad0112

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