User: tim.ivanov.92

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Posts by tim.ivanov.92

<prev • 62 results • page 1 of 7 • next >
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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 4 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 4 months ago by tim.ivanov.9210 • updated 4 months ago by Carambakaracho1.8k
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Comment: C: Protein coding annotation from UCSC
... Thank you, that does it! ...
written 4 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 4 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 4 months ago by tim.ivanov.9210 • updated 4 months ago by Luis Nassar150
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Comment: C: Annotating multiple sequence alignment
... ok, thank you anyway! ...
written 8 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 8 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 8 months ago by tim.ivanov.9210 • updated 8 months ago by Asaf6.3k
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Comment: C: Convert MAF to FASTA
... Thank you for the second link - i'll look into it Do you mb know how to get complete UCSC fasta records by **droSec1.super_9**? I think i will need it anyway later ...
written 9 months ago by tim.ivanov.9210
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Comment: C: Convert MAF to FASTA
... Does it considerer blocks inside an alignment? cos thats the whole problem - different blocks may include different organisms ...
written 9 months ago by tim.ivanov.9210

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