trouble in blasting the seq file

Question

[oliya]

hello there, Can I use BLAST2go software to blast about 80000 sequences at a time and for functional analysis like GO, KEGG??? the sequence that I have is(seq>= 200 base paired ) in fasta format and assembled in trinity.

I tried in BLAST2 go pro but got problem while blasting as sequence file is big.

could you please suggest me the suitable way to deal???

[giroudpaul]

I don't know Blast2Go specifically, but maybe reducing the number of sequences you provide as it seems to be the problem (for example 8 times 10000 sequences instead of 80000 at once) ?

[untitpoi]

Hi, Blast2go is not suitable for blasting sequences: it will take a long long time as you may have noticed. I recommend to go on local using NCBI-blast for the blast and use a cluster if your instutition owns one. You can get more info on the NCBI website.

Answer 1

[natasha.sernova]

Make a database and search inside the database with blastn, for example.

1) First you need to make a database from your nucleotide sequences.

To do this:

makeblastdb -in input_file (file-name of the contigs or whatever) -dbtype nucl (if nucleotide) -out dbname (the database name)

Use input file in *.fa-format.

2) Run the blast-program:

blastn -query input (with the gene file) -db (database name, which was created in step 1) -out outname (file name with the results)

So use blastn for this search in the nucleotide database. You said you know the sequence of needed gene in the genome?

Hopefully the size of the database will not be the bottle neck.

Good luck!