BlastX qstart qend coordinates

Question

[pooryamb]

Dear all,

In my study, I have come across a problem. I would appreciate it if someone could double-check the issue. I see in some cases BlastX does not give the correct coordinates of the qstart, and qend which show the start of the alignment in query and the end of alignment in query, respectively.

For instance, I used the following as the query:

GGGAAGAATGAATAGAGGTGAGCTTAAACAATATAAATATGATTTGGCATGTATTTACGTGTCTTTACATTTCACGCGTCTCTGTTTCACCCTTTATTTATTTTCCCGCCAGTGTCTCGGGGACGTATGCGATTTTGGTGGCAACACCGGTGCACAGGGGGGAAGGTTCGCATGCTTTATTCACAAAGTGCACACACACACACATCCATACACACACGCAAACACACACACACACAAGCGCACACGCATATATATACATATATATATATATATATGTATATTTTGGTGGATAAAACTTAATTATCATATTAACTATTCAAGCAACACAGGGAGGGTAGCAGCAACGGCAACAGACCAAACAAGAGTGAAAAAAGGAAAAAAAATGAGTAAAGTGGAAAATGAAATGAGATGAAACGGATAAACAACATTTTTCCTTTTTTCTTCTTTCAGCGGTTTTTAGCGTGTGAGTTTGAAGAGACCTTTCTCACTACATACGCACACTCCTTTCCCCTCCCCCGCTGCAACATAATGCCTAACACGAGCACGTATGGAACTGCCCAGTTAAAAGGACTCAAAACGTAAAAGAAAAAAAAAAGAGAGAAGGGGAGGGGGGAAAAACAGACGAAAATAGGAACAAAGACAGAAAAGAACGAGCAGCAATACAACAGTAACAAAAGGAAAACGTGTTTCATGCGCAAGAAAAAGGAAAAATTGGAGGAAGAGAAGGAGGAGGAGGGGAAACGAGCGTGGAATTTTCTTCTCATTGCTTCCGCGCCTCCAATTGGTACAGCCGTACGGCACAACCCTTCCTTCCTTCTTTTCATTCTTTTTTTGGAGGAGGAAGAGGGGAGGGAACGCTCCGCGCGGCGCAAAAAAAAAAAAAGAAGAAAGAAATCCCCTTCTCTTGCTTATTTGCAAACTCGACTTCAAACATAAACAAAAAACAAACAACCTTCCACAAAGACGCGCAGACACAAATCCGCCGATGCGCTCGCAGGAAGATGGATTCGCAAGCATACAAGTTTTTTTTTTTTAATTCCCACCCTTCTCTCCTTCCCCCCTCAT

and the following sequence as the target:

MLANPSSCERIGGFVSARLCGRLFVFCLCLKSSLQISKRRGFLSSFFFFAPRGAFPPLFLLQKKNEKKEGRVVPYGCTNWRRGSNEKKIPRSFPLLLLLFLQFFLFLAHETRFPFVTVVLLLVLFCLCSYFRLFFPPPLLSFFFLLRFESF

The reverse complement of the position 562:1017 of the query matches with the target. However, BlastX reports 1017 and 628 as the range of the query matching to target. I used version 2.9 and 2.12 of the blast+ and the online blast tool. All gave me the same numbers.

Answer 1

[Mensur Dlakic]

This is because of low-complexity region masking. You have several of those in the subject protein, but in particular one is at the very end. When those regions are somewhere in the middle and the alignment can still be extended past it, they will be shown as lower-case letters but won't disrupt the alignment. When the low-complexity region is at either end, I think the alignment will not include that part.

If you uncheck low-complexity in "Algorithm parameters" I think you will get the whole region aligned.

[pooryamb]

Thanks, You are right!

[pooryamb]

Could you please help me to deactivate low-complexity masking? What should I add to my command to disable low-complexity region masking for blastx?

[Mensur Dlakic]

If you are talking about command-line version of blastx, you need to add -seg no to the rest of your parameters. blastx -help will list all the options.