Concatenate FASTA seqs accroding to species

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4.5 years ago

c_gomez • 0

Hey all!

I have a very easy task to do with my sequences but my knowledge on managing fasta files by bash command is not big enough to deal with this :( I'd truly appreciate your help with this. So to the point, this is the issue:

I have 2 multifasta files, in which the headers are like >SEQID_SPECIES. I wan to merge both files to create a new multifasta file in which the sequences are concatenated according to the species. For example:

Inputs:

>SEQ1_ECOL

ACGT

>SEQ2_ECOLI

AAAA

Output:

>NEWSEQ_ECOLI

ACGTAAAA

Any ideas on how to do this?

If easier: I could also use the seuqneces concatenated just by order, i.e. the first sequence of file 1 concatenated with the first one of file 2 and so forth... Also, I care neither about the header of the merged sequences nor about the sequences with no match.

Thanks in advance!

fasta bash sequence concatenate • 861 views

ADD COMMENT • link 4.5 years ago by c_gomez • 0

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Entering edit mode

Asked several times before, e. g.:

How to concatenate two fasta files, using regular expressions

Concatenate Two .Fasta Files Into One

ADD REPLY • link 4.5 years ago by h.mon 35k

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