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zhaoyanswill / RAPSearch2

Reduced Alphabet based Protein similarity Search
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Alignment coordinates error #31

Open bachev opened 7 years ago

bachev commented 7 years ago

Hi,

I have noticed a weird error in coordinates for DNA queries and attached a minimal example which demonstrates this.

rs_coordinates_error.tar.gz

In the attached example, "query_r.fasta" is the reverse complement of "query.fasta". Both are searched against "sbjct.fasta". And the results look like this:

So, query vs RIBBA_BACSU gives: Query: 139 FHPIEE...LGHLLHF 1329 .......... FHPIEE...LGHLLHF Sbjct: . 2 FHPIEE...LGHLLHF 398

while query_r vs RIBBA_BACSU gives: Query: 1314 FHPIEE...LGHLLHF 124 ........... FHPIEE...LGHLLHF Sbjct: .. 2 FHPIEE...LGHLLHF 398

That is, both searches return the exact same alignment, but notice the query coordinates:

Bastien

zhaoyanswill commented 7 years ago

Thank you for using RAPSearch2! I’ll look into it!

On Sep 27, 2016, at 1:17 PM, Bastien Chevreux notifications@github.com wrote:

Hi,

I have noticed a weird error in coordinates for DNA queries and attached a minimal example which demonstrates this.

rs_coordinates_error.tar.gz https://github.com/zhaoyanswill/RAPSearch2/files/496360/rs_coordinates_error.tar.gz In the attached example, "query_r.fasta" is the reverse complement of "query.fasta". Both are searched against "sbjct.fasta". And the results look like this:

So, query vs RIBBA_BACSU gives: Query: 139 FHPIEE...LGHLLHF 1329 .......... FHPIEE...LGHLLHF Sbjct: . 2 FHPIEE...LGHLLHF 398

while query_r vs RIBBA_BACSU gives: Query: 1314 FHPIEE...LGHLLHF 124 ........... FHPIEE...LGHLLHF Sbjct: .. 2 FHPIEE...LGHLLHF 398

That is, both searches return the exact same alignment, but notice the query coordinates:

once (139, 1329) once (1314, 124) Bastien

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