Use different penalty scores for two ends of the DNA sequence

[misik]

Hi,

I'd like to ask for a feature request if it is feasible to do. I'd like to align a ~23 bp sequence to genome and find all similar sequences upto a certain mm/gap level. I already use glsearch36 for this type of search and parse the results of -m BB to look like:

CATTGCTAGACTTGACCCACNRG CATTGCTAGACTTGACCCACAGG ||||||||||||||||||||||| 0 0 0 0 0 0
CATTGCTAGACTTGACCCACNRG CATTGCCAGACTTGACCCACAA- ||||||.|||||||||||||||~ 1 1 0 1 0 1
CATTGCTAGACTTGACCCACNRG CATTGCCAGACTTGACCC-CGGG ||||||.|||||||||||~|||| 2 1 1 0 0 0

I'd like to have the option to have "NRG" or another selected sequence at the 3' or 5' end of the aligned query sequence to have a different penalty for mismatches and gaps. Currently I modified the mm penalty matrix and I use "NRK" and assign different penalties for R and K, but this may have some side effects if K is used for other sequences in the query. Is it possible to have two separate penalty matrices for the two parts of the sequence or any other way to implement this?

Thank you,
Meltem

[wrpearson]

I will be away so I will not be able to answer your question completely, but one strategy you might try is using a PSSM with different weights at the ends. Bill Pearson On Aug 30, 2021, at 12:29 PM, Meltem Isik ***@***.***> wrote:  Hi, I'd like to ask for a feature request if it is feasible to do. I'd like to align a ~23 bp sequence to genome and find all similar sequences upto a certain mm/gap level. I already use glsearch36 for this type of search and parse the results of -m BB to look like: CATTGCTAGACTTGACCCACNRG CATTGCTAGACTTGACCCACAGG ||||||||||||||||||||||| 0 0 0 0 0 0 CATTGCTAGACTTGACCCACNRG CATTGCCAGACTTGACCCACAA- ||||||.|||||||||||||||~ 1 1 0 1 0 1 CATTGCTAGACTTGACCCACNRG CATTGCCAGACTTGACCC-CGGG ||||||.|||||||||||~|||| 2 1 1 0 0 0 I'd like to have the option to have "NRG" or another selected sequence at the 3' or 5' end of the aligned query sequence to have a different penalty for mismatches and gaps. Currently I modified the mm penalty matrix and I use "NRK" and assign different penalties for R and K, but this may have some side effects if K is used for other sequences in the query. Is it possible to have two separate penalty matrices for the two parts of the sequence or any other way to implement this? Thank you, Meltem — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub<#33>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ABQYNPZAYZDAKSINVVMYFQLT7PEZ5ANCNFSM5DCN3CMQ>. Triage notifications on the go with GitHub Mobile for iOS<https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android<https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>.