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#SID giving wrong sequence ids for VMSP & VGEN algorithm
Posted by: Tarun Madan
Date: October 10, 2017 09:21AM

Hi,

I ran VMSP and VGEN algorithm on a set of sequences. In the sequences that i got as the result, the sequence ids i.e. #SID are wrong for single length sequences. There are some additional entries in the sequence ids list.

eg: 300 -1 #SUP: 68324 #SID: 2 11 12 13 24 25 26 27 29 31 32 33 34 39 ......

It includes some sequence ids which don't have 300 -1

while for multi-length item sequences like

501 -1 518 -1 #SUP: 66286 #SID: 16 20 42 64 66 .....

the list of sequence ids is correct.

Has anyone else encountered such an issue?

Thank you

-Tarun

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Re: #SID giving wrong sequence ids for VMSP & VGEN algorithm
Date: October 10, 2017 08:42PM

Hi Tarun,

You may have discovered a bug!

Could you please send me your input file with the algorithm named and parameters that you have used to my e-mail? philfv8 AT yahoo DOT com

Then, I will try to see what is the problem. It seems like a bug. Then, i will fix it.

Best,

Philippe

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Re: #SID giving wrong sequence ids for VMSP & VGEN algorithm
Posted by: Tarun Madan
Date: October 11, 2017 02:27AM

Hi Philippe,

I have shared with you the input file and parameters used over the email.
Thank you!

-Tarun

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