User: gorilla.in.a.tie

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Posts by gorilla.in.a.tie

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Comment: C: Strange reference allele convention
... Agree with you both, but have accepted this answer as it confirmed my suspicion about what was going on ...
written 9 weeks ago by gorilla.in.a.tie20
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Strange reference allele convention
... Hey all, I downloaded the accompanying snps from the paper: **[Genome-wide identification of splicing QTLs in the human brain and their enrichment among schizophrenia-associated loci][1]** Atsushi Takata, Naomichi Matsumoto & Tadafumi Kato but found some strange alignment to the reference g ...
alignment snp written 9 weeks ago by gorilla.in.a.tie20 • updated 9 weeks ago by Kevin Blighe33k
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Comment: C: Gap penalty in smith waterman
... So what you are saying is that it is necessary to calculate gap penalty for a given base matching, and use replacement base context? Do you have a sense of how people are generally coming up with the substitution matrices for smith waterman dna local alignment experiments - it seems to be mostly jus ...
written 4.1 years ago by gorilla.in.a.tie20
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Gap penalty in smith waterman
... Hi all,   I am looking for advice on how to calculate the gap and affine gap extension penalties that are used in the dynamic programming approaches to sequence alignment. I understand that the substitution matrices are simple lod scores, but always see somewhat hand wavy justifications of gap pen ...
sequence alignment written 4.1 years ago by gorilla.in.a.tie20 • updated 4.1 years ago by Istvan Albert ♦♦ 78k

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Popular Question 4.1 years ago, created a question with more than 1,000 views. For Gap penalty in smith waterman

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