User: tim.ivanov.92

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Posts by tim.ivanov.92

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Genome sequence from protein
... I've done tblast of a certain protein and got a list of hits. Is there a way to programmatically extract genomic regions for my hits? I'm using biopython mostly ...
genome sequence alignment written 5 days ago by tim.ivanov.920
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Comment: C: Getting genomic regions by local coordinates (protein/transcript)
... It can, but do you know if it is possible to switch automatically to different organism/assemblies? It seems like the same problem here as with cruzdb - you can easily do it if you know the organism and assembly, but if you have only blast record - can you generate a url for reference? ...
written 6 days ago by tim.ivanov.920
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Comment: C: Getting genomic regions by local coordinates (protein/transcript)
... unfortunately, we are talking about fruit fly dm3 and also i need a command line tool - a web server would be hard to implement in a pipeline ...
written 6 days ago by tim.ivanov.920
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Comment: C: Getting genomic regions by local coordinates (protein/transcript)
... Thank you, yes, that can answer my problems. But does ensemble has drosophila melanogaster assemble version 3, instead of 5 and 6? I am working with this assembly and using a liftover as an extra step would be a complication toa pipeline ...
written 6 days ago by tim.ivanov.920
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Comment: C: Getting genomic regions by local coordinates (protein/transcript)
... 1) I've made tblast of a certain protein and have a list of alignments of my reference protein. 2) With accession numbers of these proteins i've download the coding sequences for them (through biopythons functions to get genbank format through accessions) and aligned them instead of proteins. 3) Kn ...
written 6 days ago by tim.ivanov.920
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Getting genomic regions by local coordinates (protein/transcript)
... What is the easiest way to transform local coordinates on a protein/transcript to genomic coordinates (given accession number)? ...
python cruzdb ucsc written 8 days ago by tim.ivanov.920 • updated 7 days ago by Emily_Ensembl15k
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Software for genome coordinates from alignment
... Is there a package/software (preferably python) for coordinate conversation from alignment to genome? For example i've done tblastx of a reference protein and obtained a number of alignments. Is it possible now to easily do any of these things: 1). Get coordinates of specific exons from reference ...
genome gene alignment written 11 days ago by tim.ivanov.920
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Exonerate output handling/settingup
... I'm trying to get maximum from [exonerate][1] aligner tool: i would like to be able to extract alignments produced automatically and be able to parse it in any way. For example - i want to know whether start/end of query/subject sequence is aligned or not. my code is like from Bio import Searc ...
exonerate alignment biopython written 12 days ago by tim.ivanov.920
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Setting up blastn to retrieve FULL query sequence
... How can i specify standalone blastn options for it to retrieve full query sequences in output? For example i have a query lengths ~(100 - 300) bp, and i'm blasting one of them (i am doing 2 by 2 blast) against subject with length ~3000bp. But in the output i have a lot of hits that are very-very sm ...
alignment blastn written 6 months ago by tim.ivanov.920 • updated 6 months ago by Jean-Karim Heriche16k
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Blast+ settings to specify region-related accuracy
... I want to set up blast (bl2seq for comparing 2 sequences) so that score of 2 sequence similarity would have a hard penalty on mismatches/gaps at both ends of sequences, and soft penalties in the middle. Is there a way to o this? ...
alignment blast+ written 6 months ago by tim.ivanov.920 • updated 5 months ago by Biostar ♦♦ 20

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