Blast problem

[shalabh sharma]

Hi All,         This not exactly a bioperl query but i thought may be its a
good place to ask.
I am using blastall to blast sequences against my in house database.

one of the query sequence is :-

>JCVI_PEP_1105095073661 /read_id=JCVI_READ_391469 /begin=1 /end=1075
/orientation=-1 /5_prime_stop=TAA /3_prime_stop=0
/orf_id=JCVI_ORF_1105095073660 /ttable=11 /length=358 /ergatis_id=7720
/sample_id=JCVI_SMPL_1103283000001 /sample_name=GS000a /number_of_sites=2
/site_id_1=JCVI_SITE_GS000_S11 /location_1="Sargasso Station 11"
/region_1="Sargasso Sea" /country_1=Bermuda /site_depth_1="5 m"

LLNQESFRATPYTSRIEKQGVTAYTVYNHMLLPAAFGSLEESYHHLKKNVQIWDVAGERQVEISGKDSSKLVQLMTCRDL

SKSKDGRCYYCPILDDEAGIINDPIVLRINENKWWISIADSDVILFAKGLAIGNKFEVKILEPNVDIMAVQGPKSFGLME

KVFGKKITELKFFDFDYFDFEGAKHLIAKSGWSKQGGYEIYVENIESGLKLYDRLFEIGKEFYIRPGCPNLIERIESGLL

SYGNDMDNGDNPFECGFDKFINLDADINFLGKEKLKKIKAEGIKKKLVGVKFDIKEISLSKSIDLKDESSNIIGELRSAC

YSPHFGKVIGIAMIKKPYCEVSQIVKAEIIIFNVKKKK


and exactly the same sequence is there in my database:


>JCVI_PEP_1105095073661

LLNQESFRATPYTSRIEKQGVTAYTVYNHMLLPAAFGSLEESYHHLKKNVQIWDVAGERQVEISGKDSSKLVQLMTCRDLSKSKDGRCYYCPILDDEAGIINDPIVLRINENKWWISIADSDVILFAKGLAIGNKFEVKILEPNVDIMAVQGPKSFGLMEKVFGKKITELKFFDFDYFDFEGAKHLIAKSGWSKQGGYEIYVENIESGLKLYDRLFEIGKEFYIRPGCPNLIERIESGLLSYGNDMDNGDNPFECGFDKFINLDADINFLGKEKLKKIKAEGIKKKLVGVKFDIKEISLSKSIDLKDESSNIIGELRSACYSPHFGKVIGIAMIKKPYCEVSQIVKAEIIIFNVKKKK


But the blast report that i am getting does not give me 100% identity, there
is some region thats not aligned (though) its exactly the same.


portion of a blast report:


Score =  665 bits (1716), Expect = 0.0,   Method: Compositional matrix
adjust.

 Identities = 341/358 (95%), Positives = 341/358 (95%)


Query: 1   LLNQESFRATPYTSRIEKQGVTAYTVYNHMLLPAAFGSLEESYHHLKKNVQIWDVAGERQ 60

                LLNQESFRATPYTSRIEKQGVTAYTVYNHMLLPAAFGSLEESYHHLKKNVQIWDVAGERQ

Sbjct: 1    LLNQESFRATPYTSRIEKQGVTAYTVYNHMLLPAAFGSLEESYHHLKKNVQIWDVAGERQ 60

---------------------------
--------------------------

Query: 241 SYGNDMDNGDNPFECGFDKFINLDADINFXXXXXXXXXXXXXXXXXLVGVKFDIKEISLS 300
                  SYGNDMDNGDNPFECGFDKFINLDADINF
     LVGVKFDIKEISLS
Sbjct: 241  SYGNDMDNGDNPFECGFDKFINLDADINFLGKEKLKKIKAEGIKKKLVGVKFDIKEISLS 300

Query: 301 KSIDLKDESSNIIGELRSACYSPHFGKVIGIAMIKKPYCEVSQIVKAEIIIFNVKKKK 358
                  KSIDLKDESSNIIGELRSACYSPHFGKVIGIAMIKKPYCEVSQIVKAEIIIFNVKKKK
Sbjct: 301  KSIDLKDESSNIIGELRSACYSPHFGKVIGIAMIKKPYCEVSQIVKAEIIIFNVKKKK 358


I would really appreciate if anyone can help me out.

Thanks
Shalabh

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[Dave Messina-3]

Hi Shalabh,

It's a low-complexity region that's being ignored (X'd out) due to the
compositional matrix adjustment that's on by default.



Dave
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