How to turn off low complexity filter in BLASTn?

Question

[biotech]

Seems command line BLASTn is segmenting some of my hits in two HSPs due to this filter, but homology is 100% for both HSPs and they overlap. Have a look at this one:

qseqid  sseqid  pident  length  mismatch    gapopen qstart  qend    sstart  send    evalue  bitscore    qcovs   qcovhsp
gi|1006752541|gb|LKUW01000052.1|:59772-65114    Scaffold_1  100.00  3428    0   0   1   3428    1245417 1241990 0.0 6331    100 64
gi|1006752541|gb|LKUW01000052.1|:59772-65114    Scaffold_1  100.00  1992    0   0   3352    5343    1241789 1239798 0.0 3679    100 37

Thanks

Answer 1

[Andrzej Zielezinski]

By default BLAST masks your query (by the -dust flag) and database (-db_soft_mask).

This is a sample BLAST command to disable all the sequence masking:

blastn -query query.fa -db db.fa -dust no -soft_masking false -outmft 6

[biotech]

Thanks for the command @a.zielezinski. Unfortunately still giving me some segmented hits, as well as some unspecific hits. Anyway, I will have to look manually at this ones.

qseqid  sseqid  pident  length  mismatch    gapopen qstart  qend    sstart  send    evalue  bitscore    qcovs   qcovhsp
M6_chromosome_2979829_2985171   Scaffold_1  100.00  3428    0   0   1916    5343    1241990 1245417 0.0 6331    100 64
M6_chromosome_2979829_2985171   Scaffold_1  100.00  1992    0   0   1   1992    1239798 1241789 0.0 3679    100 37

Answer 2

[Medhat]

Filtering: Some of the BLAST programs mask regions of low complexity by default. These regions are not allowed to initiate alignments, so if your query is largely low complexity, the filter may prevent all hits to the database. On the Basic BLAST pages, adjust the filter settings in the section 'Filters and Masking', under 'Algorithm parameters'. For a description of low complexity filters, see "What is low-complexity sequence?"

http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=FAQ#nohits

[microfuge]

Maybe not of much use but the legacy blast does have that options -F F

-F Filter query sequence (DUST with blastn, SEG with others) [String] default = T

[biotech]

Do you think it's possible to turn this off? Can't find this option in BLAST 2.2.31+.

[Medhat]

from command line I think you can change dust default value from 20 64 1 to no

http://www.ncbi.nlm.nih.gov/books/NBK279675/