BLAST server

[SDPA_Pet]

Hi, I was wondering if there is online free server that can blast big data sets?

Thanks

[A.N.Other]

That you upload your large dataset to in order for the server to allow you to BLAST it? Is there any particular reason you can't download the BLAST+ suite and do it locally?

[SDPA_Pet]

Yes, I know offline BLAST+ can do this. However, I don't have a good cluster computer to do this. So, that is why I ask if there is any free online super computer that I can use.

[rhinoceros]

There are free services for some specific purposes. What might your data set be?

[SDPA_Pet]

My data set is 454 microbial metagenomics data. I would like to do BLASTX against nr database. Maybe also BLASTN.

Thanks

[rhinoceros]

Upload it to MG-RAST then. You can later extract tabular output against lots of different dbs. Register an account and have a look at some publicly available set, especially the download page..

[SDPA_Pet]

Hi Rhinoceros,

I did that. I need to use BLASTX is because I would like to use MEGAN to do some analysis. I posted topic couple of days ago about MGRAST-MEGAN. I think you saw it.

Currently, there is no good way to convert mgrast annotation to NCBI format. (MG-RAST support said this).

So, I need to BLAST my data set.

[rhinoceros]

Hi Rhinoceros,

Currently, there is no good way to convert mgrast annotation to NCBI format. (MG-RAST support said this).

I'm surprised. If you go for example here, scroll down to "Annotation Download via API", select "feature" for annotation type and GenBank for data source and click download, you'll end up with the file "mgm4447970.3_feature_GenBank.tab", which looks like:

query sequence id	hit m5nr id (md5sum)	percentage identity	alignment length,	number of mismatches	number of gap openings	query start	query end	hit start	hit end	e-value	bit score	semicolon seperated list of annotations
mgm4447970.3|GF8803K01BBK1N	0001e05fd22fb2fee5c66d3bfc20f4d7	62.86	140	52	0	16	155	602	741	2.2e-40	163.0	ABK03889.1
mgm4447970.3|GF8803K01C9I15	0001e05fd22fb2fee5c66d3bfc20f4d7	66.67	69	23	0	79	147	400	468	9.5e-18	88.0	ABK03889.1
mgm4447970.3|GF8803K01DKQT4	0001e05fd22fb2fee5c66d3bfc20f4d7	78.12	32	7	0	1	32	461	492	2.0e-07	54.0	ABK03889.1
..

Now if you remove the first line and do:

awk '{print $1"\t"$13"\t"$3"\t"$4"\t"$5"\t"$6"\t"$7"\t"$8"\t"$9"\t"$10"\t"$11"\t"$12"\t"}' mgm4447970.3_feature_GenBank.tab

Output is:

mgm4447970.3|GF8803K01BBK1N	ABK03889.1	62.86	140	52	0	16	155	602	741	2.2e-40	163.0	
mgm4447970.3|GF8803K01C9I15	ABK03889.1	66.67	69	23	0	79	147	400	468	9.5e-18	88.0	
mgm4447970.3|GF8803K01DKQT4	ABK03889.1	78.12	32	7	0	1	32	461	492	2.0e-07	54.0
..

Which looks a lot like tabular blast output to me ('qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore'). If it doesn't work as such, you should read MEGAN's manual carefully, especially the part about file formats and what it actually parses from tabular blast output. Also, I don't know if the e-values and bitscores are "proper", but if there is an "error", at least it should affect all the hits the same way.

[AndrewRGross]

I'd like to look for functional genes on someone else's metagenome on MG RAST. I know I can search for annotated genes, but is there a way to do an alignment type search against data on the MG-RAST server?