Question: How Can I Batch Blast Sequences To Identify Them?
3
gravatar for John
8.9 years ago by
John770
John770 wrote:

I have a list of 189 Accession numbers for 16s rRNA, how can I batch BLAST these to find which species they are closest too? I tried this server: http://greengene.uml.edu/programs/NCBI_Blast.html but the output that it gives me is huge for each accession number. I'm more looking for the a program that will give me a summary so I can quickly see the species that most match these 189 sequences.

Thanks, John

rrna sequence blast • 7.9k views
ADD COMMENTlink modified 4.0 years ago by Antonio R. Franco4.3k • written 8.9 years ago by John770
4
gravatar for Neilfws
8.9 years ago by
Neilfws48k
Sydney, Australia
Neilfws48k wrote:

Most online BLAST servers do not permit batch BLAST. It's unfortunate that whilst the Greengenes server is an exception to this, it does not allow you to specify a couple of key BLAST parameters: -v (number of hit descriptions to display) and -b (number of alignments to display). Setting each of these to 1 would show you only the first hit.

Batch BLAST generally requires that you set up BLAST locally. You would have to download unaligned sequences in fasta format from this location. BLAST databases are generated using the program formatdb, part of the BLAST executables package available from NCBI. It's not too difficult; there are plenty of questions and answers regarding local BLAST configuration at this site.

An alternative might be to use an aligner such as BLAT: see executables and source at Jim Kent's site. This will allow you to align your queries with the Greengenes sequences (both in fasta format), in memory. You'll need to look at the headers in the Greengenes sequence file to make sure they contain the information you need in the output.

ADD COMMENTlink written 8.9 years ago by Neilfws48k
2
gravatar for David W
8.9 years ago by
David W4.7k
New Zealand
David W4.7k wrote:

Have you looked at PLAN, (described here)

It's a web-service that allows you to BLAST sequences, filter results accordingly, then export annotations etc. (Been a long time since I've used it, so not sure if it'll work for your case)

EDIT: Went back and found my PLAN account details - it'll definitely do what you want but you have to upload FASTA files (not just IDs). Once you fetched the FASTA sequences and clicked "Do BLAST" it's pretty straightforward.

ADD COMMENTlink modified 8.9 years ago • written 8.9 years ago by David W4.7k
1
gravatar for Kevin
8.9 years ago by
Kevin630
Kevin630 wrote:

You can use Biopython to submit the blast jobs either locally or via the web depending on data requirements.

you probably should use a program like MEGAN http://genome.cshlp.org/content/17/3/377.full

ADD COMMENTlink written 8.9 years ago by Kevin630
0
gravatar for Antonio R. Franco
4.0 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.3k wrote:
Use Blast2Go The Free version is very nice
ADD COMMENTlink written 4.0 years ago by Antonio R. Franco4.3k
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