BOL: Question: How to extract sequence from a multifasta file?

Question: Question: How to extract sequence from a multifasta file?

Neel
2870 days ago

Question: How to extract sequence from a multifasta file?

Extract "Seq2" from the list below
>Seq1
GTGCACTAAGAAAAATAAAATTTGTTCTTTTAAGATAATCATTTC
CTGGACGAATATCAATAGCAATAGAATAAGTCCAATCAAATGAT
TGCCGTGATGAACGAACTTGTAATTGTTGATAACTAGAACCAT
GCTGTAAACAAAATTTTGATGACCATTGTGGTCGACCTTCTTGT
TGACGATGTAAACCATTTCCAACTCGCATAACACATGTATTATTA
CGCTGAGCATTATCGAAAGAAAGAAGAAGT
>Seq2
CAGGGCCAGCGCCGCCGACAGGCCGGTGAAGCCGCCGCCGA
CGATGGCCACGTCCACCTGCGCCGGCAGGTCTTGCGACCGCG
GCACGAAGGCGGGGGCGGAATCGGTCCAGTACGGGTCGAGCT
TCATGGCGGCGGCGAGGGGCGGGAAGGGCAGCGTTCGATCAG
GGGCCGGGGTTCAGAGACCCACCACGCCGGGCAGGCCGCCGA
TGTCCTGGATCTCGACATAGCGATAGGCCGGGTTGCCCGGGC

Answers

Try samtools

$ samtools faidx multifile.fa

$ samtools faidx multifile.fa Seq2 > Seq2.fa

Jit 2870 days ago

I always try faSomeRecords, to extract. It is lil handy.

See BIOCONDA https://bioconda.github.io/recipes/ucsc-fasomerecords/README.html

Shruti Paniwala 2870 days ago

This seems interesting tool indeed. The BIOCONDA name is funny ;)

— Abhimanyu Singh 2870 days ago

You can also try this, if you have lists of ids

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

Abhimanyu Singh 2870 days ago

BOL

Neel

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Question: Question: How to extract sequence from a multifasta file?