[Bioperl-l] translation frame problem in bioperl

shalabh sharma shalabh.sharma7 at gmail.com
Mon Jul 2 13:09:57 EDT 2012


Hi All,
         I am just confused about the translation frames. I used bioperl to
parse a blastx report.
Reports shows that the frame used is -2 but when i translate the sequence
using EMBOSS or Some other program the frame is -1.
Am i doing something wrong here.

Here is the sequence:
>gi|378759230|gb|AHBJ01000169.1| SAR86 cluster bacterium SAR86D
scf1120176765857, whole genome shotgun sequence 2642:3697
AGCTTCCCATGGAACCCATGCAAGTGCAATATTTGTTTCTAGCTCTGGTGACCACCAAGGAGATGTCACGTAGCCCACCTCATCTTCATCAGTATTAGTTACTATCCAAAAATCAGAAGCATAATCTGTGATTTCTTTTCCTCCAAGGGTTAAACCAACCATCTTCATTTTAAATGGTGCATTTCCTTCATCTATGATTGCTCTCTGTTTTTCAAGCTCTTCTTTACCAATGTAATCAGCTGCTTTATTTCTTGGTACCTGATAACTTAAATTAACCTGAAAGGGAGAAGTTTCATGATCCAGATCTTGTCCCCAAGACAAAATTCCAGCTGCAATGCGACGATGATGCGCAGGAGCTATGACCATTAAGCCAAATTCTTCTCCAGCCTCAAGAACAGCATTCCACATTTTTTCTGCATTATCATGTGCGTCACGAACATATATTTCATAACCTTTTTCGCCTGTAAAACCAGTTTGACTGATTACACAATCAGCTCCACCAACCTGAGTTTCTAAAATTCCATAATAAGGAACTTCTCTTAACTCTTCGCCAGCTAACTTTGCCATAAGATCTTCAGATAAAGGGCCTTGAATTTGAACAGGACAAACATCAATCTCATCAATTTCTACGTCATATTTTTTAGACACATTTACGCCTTGAAGCCAAAGTAAGAGATCGCTGTCTGATATTGAGAACCAGAATTCATCTTCTGTTAGTCTTAATAGAACAGGGTCATTTAAAACCCCTCCTTTTTCATTGCATAAAATCGCATATTTACCATTTCCGGGTTTAATTTTTGTAGCATCACGAGTTATTACATAATCTGTAAAAGCTTCTGCATCTGGACCTTTTACTCTTATCTGTCTTTCAACAGCAACATTCCACATAGTAACTCTATTAACCAAGGCTTCGTATTCAACCATGGCACCGCCATCTTCAGGTTTTACATAGCCTCGTGGATGATAAATTCGATTATATACAGTTGCTCTCCAACAGCCCGCTTCATGAGATAGATGCCAAAAAGGCGATTTTCTTACCCGGGTTGAAATTAATAA

This is a part of blast report by bioperl:
>JCVI_READ_1105499496127 /Indian_Ocean/gcvT
          Length = 352

 Score =  655 bits (1690), Expect = 0.0
 Identities = 311/352 (88%), Positives = 329/352 (93%)
 Frame = -2

Query: 3697 LLISTRVRKSPFWHLSHEAGCWRATVYNRIYHPRGYVKPEDGGAMVEYEALVNRVTMWNV
3518
            +LISTRVRKSPFWHLSHEAGCWRATVYNRIYHPRGY+KPEDGGAMVEY+ALVNRVTMWNV
Sbjct: 1    MLISTRVRKSPFWHLSHEAGCWRATVYNRIYHPRGYIKPEDGGAMVEYDALVNRVTMWNV 60
 .....
.....
Query: 2797 GLTLGGKEITDYASDFWIVTNTDEDEVGYVTSPWWSPELETNIALAWVPWEA 2642
            GLTLGGKEITDYA DFW+V + D   +     PWWSPEL TNIAL WVPW A
Sbjct: 301  GLTLGGKEITDYAPDFWLVADMDGMMLDISLPPWWSPELNTNIALGWVPWSA 352

This is EMBOSS output (from EBI):

>EMBOSS_001_4
LLISTRVRKSPFWHLSHEAGCWRATVYNRIYHPRGYVKPEDGGAMVEYEALVNRVTMWNV
AVERQIRVKGPDAEAFTDYVITRDATKIKPGNGKYAILCNEKGGVLNDPVLLRLTEDEFW
FSISDSDLLLWLQGVNVSKKYDVEIDEIDVCPVQIQGPLSEDLMAKLAGEELREVPYYGI
LETQVGGADCVISQTGFTGEKGYEIYVRDAHDNAEKMWNAVLEAGEEFGLMVIAPAHHRR
IAAGILSWGQDLDHETSPFQVNLSYQVPRNKAADYIGKEELEKQRAIIDEGNAPFKMKMV
GLTLGGKEITDYASDFWIVTNTDEDEVGYVTSPWWSPELETNIALAWVPWEA
>EMBOSS_001_5
INFNPGKKIAFLASIS*SGLLESNCI*SNLSSTRLCKT*RWRCHG*IRSLG**SYYVECC
C*KTDKSKRSRCRSFYRLCNNS*CYKN*TRKW*ICDFMQ*KRRGFK*PCSIKTNRR*ILV

......

You can see its a frame -1.

I would really appreciate your help.


Thanks

Shalabh

-- 
Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636



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