paired end nextgen DNA sequences and BLAST

[wlangdon]

Is it possible to use ncbi BLAST on paired end sequences?
I am using BWA or Bowtie2GP at present but it would be nice to
compare against a "gold standard", which I thought would be BLAST.
However I cant find anything about paired end sequences and blast.
It would be nice to take a few sequences and check the new tools
come up with similar answers.

Just wanted to double check I was not missing something obvious,

Bill

http://www.cs.ucl.ac.uk/staff/W.Langdon/

[jimmybee]

BLAST is a local aligner and primarily a database searching tool, rather than an a short-read alignment tool.

BWA and Bowtie would probably be the "gold standard" in this area

[winsettz]

bowtie was intended for the early NGS platforms that had short reads. Bowtie2 is intended for the newer NGS platforms with somewhat longer reads (like the MiSeq's ~150 nts).

One could also use mummer and mummerplot, but I'm not sure if it's an exact solution.

[wlangdon]

Dear jimmybee and winsettz,
Thank you for your helpful replies.
I could not find a switch or option on BLAST for paired end sequences, so
I guess I am right in assuming it cannot deal directly with them.
Instead I have taken a small number of Bowtie2GP matches and double checked them
with smith_waterman. (Of course this does not help where a match should have been
found but was not reported.)
Thanks again
Bill

http://www.cs.ucl.ac.uk/staff/W.Langdon/