User: tim.ivanov.92

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Posts by tim.ivanov.92

<prev • 64 results • page 1 of 7 • next >
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Comment: C: Custom substitution matrix in biopython pairwise2 aligner
... Yes! Thank you very much! ...
written 5 months ago by tim.ivanov.9210
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Custom substitution matrix in biopython pairwise2 aligner
... Is there a way to use custom matrix for nucleotide aligner in Biopython pairwise2 module? I want to decrease penalties for A->G, C->T substitutions. import Bio from Bio import pairwise2 seq1='AGTCGATCATCGGA' seq2='ATTAGATCATCGGGGA' alignment = pairwise2.align.lo ...
pairwise2 alignment biopython written 5 months ago by tim.ivanov.9210 • updated 5 months ago by tamerg80
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Comment: C: Exonerate raw score to percent identity
... Thank you, that helps - i forgot about ryo option because i was using biopython's wrapper to parse the output. Since we are here - do you know if i am able to access ryo format options from biopython? ...
written 16 months ago by tim.ivanov.9210
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Exonerate raw score to percent identity
... Does anyone know what exactly does line “raw score” in [exonerate][1] output mean? For example I attach here a screenshot of a full hit, where the length of a query is 74bp, yet the raw score is 370, which is much greater than 74. The original command was: exonerate --verbose 0 -E --model affine:b ...
smithwaterman exonerate alignment written 16 months ago by tim.ivanov.9210 • updated 16 months ago by Carambakaracho2.2k
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Comment: C: Protein coding annotation from UCSC
... Thank you, that does it! ...
written 16 months ago by tim.ivanov.9210
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Comment: C: Protein coding annotation from UCSC
... yes, sry, fixed it in the original post - now the second picture is the right one ...
written 16 months ago by tim.ivanov.9210
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Protein coding annotation from UCSC
... How do i download **only protein-coding** genes from UCSC table browser? I've chosen gencode v19 and genes and gene prediction in settings bars, but i'm getting in the result much more genes, than just protein coding I'm attaching here screenshots with my settings and the head of resulting data ...
annotation ucsc written 16 months ago by tim.ivanov.9210 • updated 16 months ago by Luis Nassar410
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Comment: C: Annotating multiple sequence alignment
... ok, thank you anyway! ...
written 19 months ago by tim.ivanov.9210
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Comment: C: Annotating multiple sequence alignment
... Thank you, this is helpful! Would you mind giving me an example of usage please? ...
written 20 months ago by tim.ivanov.9210
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Annotating multiple sequence alignment
... Does anyone know know how to use [TEXshade][1] package? Specifically, i want to just highlight some specific regions inside my alignment (exons) [1]: http://ctan.math.utah.edu/ctan/tex-archive/macros/latex/contrib/texshade/texshade.pdf ...
maf texshade alignment written 20 months ago by tim.ivanov.9210 • updated 20 months ago by Asaf8.4k

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