How to retrieved protein Fasta sequence from accession number by Entrez
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5 weeks ago
Nelo • 0

AF131201
AF326487
AF326488
AF326489
AF326490

This are the some the accession number of protein. Firstly i dont know what kind of accession number is this. beacuse usually protein accession number start with XP_/NP_. Problem arise when i try the following command using the accession number given above:

  1. esearch -db protein -query "AF131201" | efetch -format fasta > output.fasta
  2. esearch -db nuccore -query "AF131201" | elink -target protein | efetch -db protein -format fasta
  3. Or directly submitting a bunch of accession number file to Entrez batch.

But i got nothing. Reason for the error is very sure due to the accession number i used. Can somebody help a way to solve this.

Thanks

protein • 456 views
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5 weeks ago
GenoMax 108k

Those are nucleotide accession numbers. You should do the following. Sequences truncated to save space.

$ esearch -db nuccore -query AF131201 | elink -target protein | efetch -format fasta
>AAD29676.1 plasma membrane MIP protein [Zea mays]
MEGKEEDVRLGANKFSERQPIGTAAQGAADDKDYKEPPPAPLFEPGELKSWSFYRAGIAEFVATFLFLYI
TILTVMGVSKSTSKCATVGIQGIAWSFGGMIFALVYCTAGISGGHINPAVTFGLFLARKLSLTRALFYII

to process multiple accessions

$ cat id
AF131201
AF326487
AF326488
AF326489
AF326490

$ cat id | epost -db nuccore -format acc | elink -target protein | efetch -format fasta

>AAD29676.1 plasma membrane MIP protein [Zea mays]
MEGKEEDVRLGANKFSERQPIGTAAQGAADDKDYKEPPPAPLFEPGELKSWSFYRAGIAEFVATFLFLYI

>AAK26757.1 plasma membrane integral protein ZmPIP1-6 [Zea mays]
MAGGTLQDRSEEEDVRVGVDRFPERQPIGTAADDLGRDYSEPPAAPLFEASELSSWSFYRAGIAEFVATF

>AAK26756.1 plasma membrane integral protein ZmPIP1-5 [Zea mays]
MEGKEEDVRLGANRYSERQPIGTAAQGTEEKDYKEPPPAPLFEAEELTSWSFYRAGIAEFVATFLFLYIS

>AAK26755.1 plasma membrane integral protein ZmPIP1-4 [Zea mays]
MEGKEEDVRLGANKFSERQPIGTAAQGAGAGDDDKDYKEPPPAPLFEPGELKSWSFYRAGIAEFVATFLF

>AAK26754.1 plasma membrane integral protein ZmPIP1-3 [Zea mays]
MEGKEEDVRLGANKFSERQPIGTAAQGAGAGDDDKDYKEPPPAPLFEPGELKSWSFYRAGIAEFVATFLF
LYITVLTVMGVSKSTSKCATVGIQGIAWSFGGMIFALVYCTAGISGGHINPAVTFGLFLARKLSLTRAIF
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Thank you so much for the help.

But some times the following text are also displayed on the terminal whenever i used the said command.

1) Can't locate Time/HiRes.pm in @INC (@INC contains: /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .). BEGIN failed--compilation aborted.

Is it necessary to download this Time-hiRes module ?

2) Unable to locate transmute executable. Please execute the following:

nquire -dwn ftp.ncbi.nlm.nih.gov entrez/entrezdirect transmute.Linux.gz gunzip -f transmute.Linux.gz chmod +x transmute.Linux

3) <PhraseNotFound>ABK60194[ACCN]</PhraseNotFound>

I am new to this kind of work. Don't know what I am asking exactly.

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Not sure how you installed Entrezdirect but it does not seem to be installed properly.

It may be simplest to use conda to install. See conda part of this tutorial: Creating workflows with snakemake and conda

conda create -n edirect entrez-direct.

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okie! I will try this

Do i have to sign in to NCBI API key ? If so why, is it necessary?

Tnq so much

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If you are planning to do number of queries then you should. See this: https://ncbiinsights.ncbi.nlm.nih.gov/2017/11/02/new-api-keys-for-the-e-utilities/

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Okay

Thank you for responding

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