Displaying TBLASTN output

sequenceserver
#1

Hi,

By default, a tblastn output of SequenceServer shows all repeated regions marked with Xs

Query 211 GEDDMKYIETLSSKQKKRLLKNLTKLQRKAEKKKHKTDEFNQDEXXXXXXXXXXXXXXXX 270
GEDDMKYIETLSSKQKKRLLKNLTKLQRKAEKKKHKTDEFNQDEKWCMKKKKKKKNELCN
Subject 2256393 GEDDMKYIETLSSKQKKRLLKNLTKLQRKAEKKKHKTDEFNQDEKWCMKKKKKKKNELCN 2256572

I would like that the output shows the actual sequence, not Xs.

Query 211 GEDDMKYIETLSSKQKKRLLKNLTKLQRKAEKKKHKTDEFNQDEkwcmkkkkkkknelcn 270
GEDDMKYIETLSSKQKKRLLKNLTKLQRKAEKKKHKTDEFNQDEKWCMKKKKKKKNELCN
Sbjct 2256393 GEDDMKYIETLSSKQKKRLLKNLTKLQRKAEKKKHKTDEFNQDEKWCMKKKKKKKNELCN 2256572

Could you please let me know which option should I use when running TBLASTN ?

Thanks
Anh-Dao

#2

Looks like -lcase_masking will do the trick.

Priyam

#3

I did use that option but I did not see the output as I mentioned above.

Anh-Dao

#4

Did you find an answer?

Priyam

#5

No, I could not get it worked.
I selected the option -lcase_masking in the “Advanced Parameters” box as you suggested.

Anh-Dao

#6

Hi Priyam,

It seems like SequenceServer itself is adding the X’s to hard mask.
If we run command-line tblastn, using default parameters, on the server that’s hosting SequenceServer, the alignment comes back soft-masked, like this:

Score = 219 bits (557), Expect = 2e-60, Method: Compositional matrix adjust.

Identities = 171/171 (100%), Positives = 171/171 (100%), Gaps = 0/171 (0%)

Frame = +3

Query 211 GEDDMKYIETLSSKQKKRLLKNLTKLQRKAEKKKHKTDEFNQDEkwcmkkkkkkknelcn 270

GEDDMKYIETLSSKQKKRLLKNLTKLQRKAEKKKHKTDEFNQDEKWCMKKKKKKKNELCN

Sbjct 2256393 GEDDMKYIETLSSKQKKRLLKNLTKLQRKAEKKKHKTDEFNQDEKWCMKKKKKKKNELCN 2256572

Query 271 erkrkYSSESECGHNKSYDKDLESNKQYLknkndfksnkdnkskdhhnhhkkrrkvhqnk 330

ERKRKYSSESECGHNKSYDKDLESNKQYLKNKNDFKSNKDNKSKDHHNHHKKRRKVHQNK

Sbjct 2256573 ERKRKYSSESECGHNKSYDKDLESNKQYLKNKNDFKSNKDNKSKDHHNHHKKRRKVHQNK 2256752

But if we run tblastn through SequenceServer, again using the default parameters against the same database, the output is hard-masked, like this:

Score E value Identities Gaps Hit frame

219.16 (557) 1.69 × 10-60 171/171 (100.00) 0/171 (0.00) 3
Query 211 GEDDMKYIETLSSKQKKRLLKNLTKLQRKAEKKKHKTDEFNQDEXXXXXXXXXXXXXXXX 270 GEDDMKYIETLSSKQKKRLLKNLTKLQRKAEKKKHKTDEFNQDEKWCMKKKKKKKNELCN Subject 2256393 GEDDMKYIETLSSKQKKRLLKNLTKLQRKAEKKKHKTDEFNQDEKWCMKKKKKKKNELCN 2256572 Query 271 XXXXXYSSESECGHNKSYDKDLESNKQYLXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX 330 ERKRKYSSESECGHNKSYDKDLESNKQYLKNKNDFKSNKDNKSKDHHNHHKKRRKVHQNK Subject 2256573 ERKRKYSSESECGHNKSYDKDLESNKQYLKNKNDFKSNKDNKSKDHHNHHKKRRKVHQNK 2256752 Query 331 XEIDLSPPNKRLRKCTNSKSHFYTENEHSCNIEDEIDLQISLCRGERVKKC 381 QEIDLSPPNKRLRKCTNSKSHFYTENEHSCNIEDEIDLQISLCRGERVKKC Subject 2256753 QEIDLSPPNKRLRKCTNSKSHFYTENEHSCNIEDEIDLQISLCRGERVKKC 2256905

How do we get rid of the hard-masking in SequenceServer so we can show lower-case letters, rather than X’s?

thanks
tyra