My experience with Bowtie2 is limited to map Illumina reads to reference genome.
have in mind that bowtie output is in sam format.
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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.
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with fasta package you can align local-local, local-global, global-global
http://fasta.bioch.virginia.edu/fast...sta_down.shtml
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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
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Originally posted by sampie View PostHi,
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
Code:-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)?
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ncbi-blast
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.
ThanksTags: None
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