User: Rvosa

gravatar for Rvosa
Rvosa570
Reputation:
570
Status:
Trusted
Location:
Leiden, the Netherlands
Website:
http://rutgervos.blogs...
Last seen:
6 years ago
Joined:
9 years, 4 months ago
Email:
5**@biostars.org

I am a bioinformaticist at NCB Naturalis, a contributor to various open source software projects and I keep myself busy thinking about computational biology, phylogenetics and evolution.

Posts by Rvosa

<prev • 30 results • page 1 of 3 • next >
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Comment: C: Gff3 Coordinate: Find Stop Codon On - Strand
... Thank you very much for your reply, this is the first time where the 'phase' thing is starting to make sense. So is it then the case that, if we have only two CDSs in the same gene, then the phase of cds2 is going to be length(cds1) % 3? ETA: if that's how it works then I can also see that the phas ...
written 6.0 years ago by Rvosa570
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Comment: C: Gff3 Coordinate: Find Stop Codon On - Strand
... Indeed it is, apologies. See how these coordinates are driving me crazy? Harumph. I meant to say 247127.. 247129 ...
written 6.0 years ago by Rvosa570
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Gff3 Coordinate: Find Stop Codon On - Strand
... Given the following GFF3, where is the stop codon supposed to be: scaffold1.1 maker gene 247127 258737 . - . ID=... scaffold1.1 maker CDS 258659 258737 . - 1 ID=... scaffold1.1 maker CDS 254856 254976 . - 2 ID= ...
gff3 codon coordinates strand written 6.0 years ago by Rvosa570 • updated 6.0 years ago by Istvan Albert ♦♦ 81k
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Preparing A Scaffolded Genome For Genbank Submission
... Hi, I am preparing a vertebrate genome for submission to GenBank (WGS). The genome is organized in scaffolds (in one big FASTA file) for which we have genes predicted by maker (GFF3 file). In communicating with the NCBI staff it emerged that their WGS submission requirements have recently shifted - ...
gff3 fasta genbank scaffolding written 6.4 years ago by Rvosa570 • updated 2.1 years ago by eennadi0
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How Do I Get A Neandertal Sequence?
... Hi, I thought this would be doable. I have a region in the human genome (chromosome number, start, stop, strand) and I know that Ensembl have aligned a consensus of the neandertal genomes against a human genome - how do I get the neandertal version for that region? Like, a FASTA file, say. The geno ...
genome fasta human written 8.6 years ago by Rvosa570 • updated 8.6 years ago by Larry_Parnell16k
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Comment: C: Is It Possible To Find For A Given Gene The Coding Sequences On Ensembl?
... Are you asking how you might go from a gene name to an ensembl gene ID? Would biomart be any help, e.g. http://www.biomart.org/biomart/martview or the perl api? ...
written 8.7 years ago by Rvosa570
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Interpreting Hyphy Testbranchdnds.Bf
... Hi, I'm trying to accomplish the following: find out the dN/dS ratio on each branch of a tree, and whether some ratios are significantly different from others, using HyPhy. Here are the steps I'm thinking about taking (in the HyPhy GUI): Standard Analyses > Positive Selection > TestBranchD ...
selection written 8.7 years ago by Rvosa570 • updated 3.6 years ago by Biostar ♦♦ 20
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Comment: C: How Can I Label Internal Branches Of A Phylogenetic Tree?
... Newick allows node labels. If you want edge labels, i.e. separate from node labels, you can use [NeXML](http://www.nexml.org). [Here is an example file](http://nexml-dev.nescent.org/nexml/examples/edgelabels.xml) with both node labels and edge labels. ...
written 8.7 years ago by Rvosa570 • updated 12 weeks ago by RamRS25k
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Comment: C: How Can I Label Internal Branches Of A Phylogenetic Tree?
... This produces (((A,B)3,C)2,D)1; by the way. ...
written 8.7 years ago by Rvosa570
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Answer: A: How Can I Label Internal Branches Of A Phylogenetic Tree?
... This can be done easily using Bio::Phylo: ``` #!/usr/bin/perl use strict; use Bio::Phylo::IO 'parse'; my $newick = '(((A,B),C),D);'; my $tree = parse( '-format' => 'newick', '-string' => $newick )->first; my $counter = 1; $tree->visit( sub { my $node = shift; ...
written 8.7 years ago by Rvosa570 • updated 12 weeks ago by RamRS25k

Latest awards to Rvosa

Autobiographer 6.0 years ago, has more than 80 characters in the information field of the user's profile.
Student 8.6 years ago, asked a question with at least 3 up-votes. For How Do I Get A Neandertal Sequence?
Popular Question 8.7 years ago, created a question with more than 1,000 views. For Interpreting Hyphy Testbranchdnds.Bf
Teacher 8.7 years ago, created an answer with at least 3 up-votes. For A: Inferring Information About The Phylogenetic Tree For A Set Of Species From A Tr
Teacher 8.8 years ago, created an answer with at least 3 up-votes. For A: Phylogeny From A Distance Matrix
Student 8.8 years ago, asked a question with at least 3 up-votes. For Distance Tree For One Million Sequences
Popular Question 8.9 years ago, created a question with more than 1,000 views. For From Ensembl Transcript Id To Go Term(S), Is There A Mapping?
Teacher 8.9 years ago, created an answer with at least 3 up-votes. For A: Sequence Evolution Library In Java
Student 8.9 years ago, asked a question with at least 3 up-votes. For Optimizing Hmmer Speed/Performance
Appreciated 8.9 years ago, created a post with more than 5 votes. For A: How Do You Manage Your Files & Directories For Your Projects ?
Teacher 8.9 years ago, created an answer with at least 3 up-votes. For A: How Do You Manage Your Files & Directories For Your Projects ?
Good Answer 8.9 years ago, created an answer that was upvoted at least 5 times. For A: How Do You Manage Your Files & Directories For Your Projects ?
Teacher 9.0 years ago, created an answer with at least 3 up-votes. For A: Alphabetic Sort In Unix/Perl With Preference On Order Of Alphabets To Be Followe

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