Best tool for the job (noob question)

[bre]

What are the best tools for aligning a query against a target with the following characteristics? I had previously tried bowtie but only got 6% alignment when over 90% was expected:

Query file:
> Format: multisequence fasta
> Number of sequences: 180,099
> Minimum sequence length: 69 bases
> Maximum sequence length: 1,045 bases
> Average sequence length: 825 bases
> Number of Ns in file: 158,231
> Longest N stretch: 363
> Number of sequences containing N: 59,998
Target file:
> Number of sequences: 1,168
> Minimum sequence length: 1,028 bases
> Maximum sequence length: 63,086,992 bases
> Average sequence length: 843,760 bases
> Number of Ns in file: 18,289,543
> Longest N stretch: 1,185,460
> Number of sequences containing N: 771

If anyone could point me in the right direction it would be greatly appreciated. Thanks!

[nilshomer]

What are the best tools for aligning a query against a target with the following characteristics? I had previously tried bowtie but only got 6% alignment when over 90% was expected:

Query file:
> Format: multisequence fasta
> Number of sequences: 180,099
> Minimum sequence length: 69 bases
> Maximum sequence length: 1,045 bases
> Average sequence length: 825 bases
> Number of Ns in file: 158,231
> Longest N stretch: 363
> Number of sequences containing N: 59,998
Target file:
> Number of sequences: 1,168
> Minimum sequence length: 1,028 bases
> Maximum sequence length: 63,086,992 bases
> Average sequence length: 843,760 bases
> Number of Ns in file: 18,289,543
> Longest N stretch: 1,185,460
> Number of sequences containing N: 771

If anyone could point me in the right direction it would be greatly appreciated. Thanks!

How about trying BLAT? It may be slow, but in this situation it may give you proper sensitivity.

[bre]

Would bwa work? I need gapped alignments which bowtie cannot do, and I'd also like to get SAM-format output.

[nilshomer]

Would bwa work? I need gapped alignments which bowtie cannot do, and I'd also like to get SAM-format output.

Since the query is up to 1Kb I would try the "bwa bwasw" command, though I have not tried it. You might have to split your queries into long and short ones. Anyone else have any advice?

[bre]

It looks right now like bfast may be my best bet. I noticed bwa doesn't allow paired-end reads for sequences longer than ~200bp.