ncbi-blast

[sampie]

Hi,

I have a trialseq.fa file having a sequence:

>trialseq
TGGCCTAACCTTCGGGAAGGAGCCGTCTAAGGCAGGGCAGATGACNNNNNNNNNNNNGTAACAAGNNNNNNNNNNNNGAACCTGNNNNNNGATCACCTCCTTTCTA

There is also a blast db having the same sequence:
makeblastdb -in trialseq.fa -dbtype nucl -out trial.db

The trialseq has been blasted agains the DB:
blastn -db trial.db -query trialseq.fa -out blast.txt

However, blast result show only a partial match:

----
Score = 84.2 bits (45), Expect = 4e-22
Identities = 45/45 (100%), Gaps = 0/45 (0%)
Strand=Plus/Plus

Query 1 TGGCCTAACCTTCGGGAAGGAGCCGTCTAAGGCAGGGCAGATGAC 45
|||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1 TGGCCTAACCTTCGGGAAGGAGCCGTCTAAGGCAGGGCAGATGAC 45

----

How to use blast in such a way that it would return true 100% match? So that N would match as any nucleotide.

Thanks

[juan.isaza]

Hi,

I have a trialseq.fa file having a sequence:

>trialseq
TGGCCTAACCTTCGGGAAGGAGCCGTCTAAGGCAGGGCAGATGACNNNNNNNNNNNNGTAACAAGNNNNNNNNNNNNGAACCTGNNNNNNGATCACCTCCTTTCTA

There is also a blast db having the same sequence:
makeblastdb -in trialseq.fa -dbtype nucl -out trial.db

The trialseq has been blasted agains the DB:
blastn -db trial.db -query trialseq.fa -out blast.txt

However, blast result show only a partial match:

----
Score = 84.2 bits (45), Expect = 4e-22
Identities = 45/45 (100%), Gaps = 0/45 (0%)
Strand=Plus/Plus

Query 1 TGGCCTAACCTTCGGGAAGGAGCCGTCTAAGGCAGGGCAGATGAC 45
|||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1 TGGCCTAACCTTCGGGAAGGAGCCGTCTAAGGCAGGGCAGATGAC 45

----

How to use blast in such a way that it would return true 100% match? So that N would match as any nucleotide.

Thanks

have you tried modifying Query filtering options?

-dust <String>
   Filter query sequence with DUST (Format: 'yes', 'level window linker', or
   'no' to disable)
   Default = `20 64 1'
 -filtering_db <String>
   BLAST database containing filtering elements (i.e.: repeats)
 -window_masker_taxid <Integer>
   Enable WindowMasker filtering using a Taxonomic ID
 -window_masker_db <String>
   Enable WindowMasker filtering using this repeats database.
 -soft_masking <Boolean>
   Apply filtering locations as soft masks
   Default = `true'
 -lcase_masking
   Use lower case filtering in query and subject sequence(s)?

[sampie]

Hi,

It seems it might be possible to get blast to work for some data set by trying various parameters. However, I contacted ncbi support and they told that handling ambiguous matches is not the strong suite of BLAST.

So, I quess it is better to just try to find a local aligner which does support ambiguous matches.

Any suggestions for a good local aligner for this purpose?

Thanks

[juan.isaza]

with fasta package you can align local-local, local-global, global-global

http://fasta.bioch.virginia.edu/fasta_www2/fasta_down.shtml

[sampie]

Thanks for suggestion.

How about bowtie2? It seem to be quite popular and good tools. From bowtie2 help I found that it can be disabled that N is considered as a negatively scoring match. However, I did not find an option to have N as positively scoring match.

[juan.isaza]

My experience with Bowtie2 is limited to map Illumina reads to reference genome.
have in mind that bowtie output is in sam format.