Is it possible to convert several protein ID in to Fasta format?
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2.0 years ago
tpm ▴ 30

Like this

1>seqid1 
MKRISTTITTTITITTGNGAG 

2>seqid2 
MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAMIEKTISGQDA
   YSHYYQPLPLVLRGYGAGNDVTAAGVFADLLRTLSWKLGV
sequence fasta • 432 views
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These are already in fasta format assuming you added 1,2 before the records.

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I did not know how I can edit properly on the question I asked, my bad :), but suppose I have 10 gene IDs, how can I fetch the fasta format?

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It will depend on what kind of ID's those are. Can you provide examples?

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For example: TATE OPPC GLSA1 RNPA RATB FTSI GALP FENR MNTR YGIS DCOR PTHC YQCA FLAW

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Please use ADD REPLY/ADD COMMENT when responding to existing posts to keep threads logically organized. SUBMIT ANSWER is only for new answers to original question.

What organism do you want to sequences from? e.g. TATE if that is the tatE protein has thousands of sequences in GenBank.

  1. Do you need the sequences for a specific organism? You can find the genome page of the organism you want at NCBI. e.g. Kelbsiella pneumoniae. All proteins can be downloaded in fasta format by using Protein link in the top box.
  2. If you just need at tatE genes then searching the protein data base would be the appropriate solution. Then use Send to drop-down at top of page to send the data to a multi-fasta file.
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I am working with an E. coli BW25113 strain. Suppose I have 200 gene IDs, is it possible to extract their fast files simultaneously? Not 1 by 1?

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  1. Here is the directory containing the proteins from this strain at Ensembl Bacteria.
  2. Download the fasta file with the sequences.

    wget ftp://ftp.ensemblgenomes.org/pub/bacteria/release-47/fasta/bacteria_87_collection/escherichia_coli_bw25113/pep/Escherichia_coli_bw25113.ASM75055v1.pep.all.fa.gz

  3. Unzip the file

    gunzip Escherichia_coli_bw25113.ASM75055v1.pep.all.fa.gz

Then use one of the solutions here to pull out genes you need: Extract fasta sequences from a file using a list in another file.

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