Is It Possible To Extract From Ncbi Nr Database Plant Protein Sequences.？

Question

[Lhl]

Hi all,

I am doing annotation of a de novo sequenced non-model plant genome. Specifically, i am annotating the genome through blastx-ing the NCBI NR database. Obviously, it will be much faster if i can draw only plant protein sequences from the large NR database. So ia m wondering if there is a way to work out that. Hope it is possible.

Elzed

[Pierre Lindenbaum]

w h y d i d y o u p a s t e y o u r t e x t a s u n i c o d e ? i t ' s u n r e a d a b l e t o m e

[Lhl]

Sorry about that. I just changed it.

Answer 1

[Jan Kosinski]

1. Go to NCBI Entrez Protein search
2. Search with all [filter] query. This will give you all protein entries
3. Locate "Taxonomic Groups" box on the right. Display tree and locate "Green plants". Click and wait a moment. You should now see proteins from green plants. The query in the Search box should change to (all [filter]) AND "green plants"[porgn:__txid33090].
4. Download everything as GI list. This is your "Plant GI list"

Now you can:

1. Download full nr database in FASTA format

2. Using a custom script select from the nr database only those entries that have a GI from the "Plant GI list"

3. Create the final plant_nr using formatdb

OR:

use new blast where apparently you can filter the nr database based on gi list using '-gilist' option of blast itself! (http://www.ncbi.nlm.nih.gov/books/NBK1763/). But I haven't used that yet.

[Lhl]

Thanks Jan. I think both of your suggestions are doable.

Answer 2

[Goldbear]

Alternatively, plantgdb maintains a uniprot-curated list of plant protein sequences.

It should be the UniProt_Protein.tar.bz2 file in ftp://ftp.plantgdb.org/download/FASTA/

This will extract out A LOT of sequence files that I wanted to join into one big file. I had to use xargs to get around the 'argument list too long' error that cat was giving me.

$ find . -type f | xargs cat > out.txt

[Lhl]

Good. But it seems that they do not have GI and accession number.