I got a 370mers sequence found in humanReferenceGenome and a RetrovirusGenome. Could any one tellme steps to evaluate possible role in the given genome?
Hi Ernesto,
You can do 6-frame translation and see if any proteins can be coded by the sequence. See the attached screenshot for the 6-translated frames. Then you can search the obtained amino-acid sequences for possible protein matches (I used CS-BLAST) . You get a perfect match in your 5'3' Frame 3 translated sequence, with a human and retrovirus protein. I think these are the sequences you are looking for. Just read about the protein in the two organisms to find out its roles, it looks like it's the reverse transcriptase, so it is responsible for translating viral RNA into DNA.
No 1 (human)
>gb|AAD51793.1| Gag-Pro-Pol-Env protein [Homo sapiens]
Length = 2294
Score = 231 bits (591), Expect = 2e-58, Method: Composition-based stats.
Identities = 103/104 (99%), Positives = 104/104 (100%)
Query: 1 MLVVGNIVIKPDSQTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASP 60
MLVVGNIVIKPDSQTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASP
Sbjct: 2071 MLVVGNIVIKPDSQTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASP 2130
Query: 61 SVHILTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVAL 104
S+HILTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVAL
Sbjct: 2131 SIHILTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVAL 2174
No 2 (retrovirus)
>sp|P63135.1| RecName: Full=Endogenous retrovirus group K member 7 Pol protein;
AltName: Full=HERV-K(III) Pol protein; AltName:
Full=HERV-K102 Pol protein; AltName: Full=HERV-K_1q22
provirus ancestral Pol protein; Includes: RecName:
Full=Reverse transcriptase; Short=RT; Includes: RecName:
Full=Ribonuclease H; Short=RNase H; Includes: RecName:
Full=Integrase; Short=IN
Length = 1459
Score = 224 bits (573), Expect = 2e-56, Method: Composition-based stats.
Identities = 104/104 (100%), Positives = 104/104 (100%)
Query: 1 MLVVGNIVIKPDSQTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASP 60
MLVVGNIVIKPDSQTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASP
Sbjct: 1148 MLVVGNIVIKPDSQTITCENCRLLTCIDSTFNWQHRILLVRAREGVWIPVSMDRPWEASP 1207
Query: 61 SVHILTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVAL 104
SVHILTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVAL
Sbjct: 1208 SVHILTEVLKGVLNRSKRFIFTLIAVIMGLIAVTATAAVAGVAL 1251
Thanks Jan, this is a free-time project. Would you like to be in collaborators list?
good! wellcome
I made an algorithm that runs in a intel corei7 searching for virus subsequences along human or animal genomes. Whenever it finds something i try to understand what role could be playing the just-found sequence
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