How to get FASTA sequences from GI number

[fefe89]

Hey guys I need help

I need to download a large amount of FASTA sequences from a set of GI number.

Is there any script to do this??

I know I could do it with http://www.ncbi.nlm.nih.gov/sites/batchentrez , but I have too many sequences (and It says to split if they are too many) and I really don't want to do it via browser


Thank you

[bt27uk]

Did you mean to cross post this in Biostars? Maybe remove the question from this list or from that list.

[fefe89]

Did you mean to cross post this in Biostars? Maybe remove the question from this list or from that list.

Since I'm blocked with this problem for a couple of days, I tryied to ask in different forums with different people in order to get an answer as soon as possible.

I can't see the problem.

If it is contrary to any rules of seqanswer, I'll delete it

[lindenb]

cross posted on biostars: https://www.biostars.org/p/112410/

[GenoMax]

One way to do this would be using blastdbcmd command that is part of the "blast" suite. You will need to have access to (or download the nt blast database indexes).

You can put a list of your GI numbers in a file like so (one per line):

$ more gi_list.txt 
4
7
78
324

$ blastdbcmd -entry_batch gi_list.txt -db /path_to/nt -outfmt "%f" -out seq_fasta_filename.fa

[fefe89]

One way to do this would be using blastdbcmd command that is part of the "blast" suite. You will need to have access to (or download the nt blast database indexes).

You can put a list of your GI numbers in a file like so (one per line):

$ more gi_list.txt 
4
7
78
324

$ blastdbcmd -entry_batch gi_list.txt -db /path_to/nt -outfmt "%f" -out seq_fasta_filename.fa

Thank you very much.

It is exactly what I was looking for!!!

[GenoMax]

Since I'm blocked with this problem for a couple of days, I tryied to ask in different forums with different people in order to get an answer as soon as possible.

I can't see the problem.

If it is contrary to any rules of seqanswer, I'll delete it

As has been said before it creates more work for folks who are answering the questions.

It is ok to cross-post but please close your post out on all forums (cross-referencing the solution, once you find one that you like).

[fefe89]

As has been said before it creates more work for folks who are answering the questions.

It is ok to cross-post but please close your post out on all forums (cross-referencing the solution, once you find one that you like).

OK. The other post has been already closed.

[piet]

I need to download a large amount of FASTA sequences from a set of GI number.

Is there any script to do this??

The recommended way to do this is with Eutils. Eutils is a Web-service offert by the NCBI.

There already exist several threads about using Eutils as well in this forum as in Biostars.

[ericaf]

One way to do this would be using blastdbcmd command that is part of the "blast" suite. You will need to have access to (or download the nt blast database indexes).

You can put a list of your GI numbers in a file like so (one per line):

$ more gi_list.txt 
4
7
78
324

$ blastdbcmd -entry_batch gi_list.txt -db /path_to/nt -outfmt "%f" -out seq_fasta_filename.fa

Hi !

I'm beginner in bioinformatics (and new on the forum) and I have the same problem as fefe89. Your answer (here above) seems totally appropriate for my problem but I have a very naive question (seems simple but I don't find an adequate answer on google) : how can I use the blastdbcmd command line if I don't want to download the (heavy) nt databases on my own computer ? Or am I forced to download the nt locally before running the command line ?

Thank you in advance for your understanding (certainly a newbies question...)

[GenoMax]

Hi !
how can I use the blastdbcmd command line if I don't want to download the (heavy) nt databases on my own computer ? Or am I forced to download the nt locally before running the command line ?

Thank you in advance for your understanding (certainly a newbies question...)

If you don't want to download the blast database locally take look at the NCBI e-utils option (referred to in one of the posts above). You will need to do some additional work to create the right query URL's.