User: db534

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db5340
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Posts by db534

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Comment: C: Retrieving homologues of human proteins using Ensembl REST API?
... Hi Pierre, This is the line of code for a *D. melanogaster* ID (FBgn0263237), which returns a result: wget -q --header='Content-type:application/json' 'http://rest.ensemblgenomes.org/homology/id/FBgn0263237?format=condensed;type=orthologues;compara=pan_homology' -O test.txt If I replace the ...
written 9 weeks ago by db5340
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Retrieving homologues of human proteins using Ensembl REST API?
... I have a question regarding the retrieval of gene homologues using the REST API of Ensembl Genomes. In particular, I am interested in the retrieval of homologues of human genes/proteins from the pan-taxonomic compara of Ensembl Genomes. However, if I supply a *Homo sapiens* gene/protein ID to the AP ...
orthologs ensembl written 9 weeks ago by db5340 • updated 9 days ago by Biostar ♦♦ 20
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Comment: C: Comparing sequence alignments using phylogenetic likelihoods?
... Thank you for reply. Indeed I am going to build a tree so I can see now that using a tree to guide selection of the alignment would be a problem. Speaking academically though, my point about lower likelihood values though is that it stops alignments of different lengths being comparable -- if a shor ...
written 2.1 years ago by db5340
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Comment: C: Comparing sequence alignments using phylogenetic likelihoods?
... The probability of an alignment being generated by this tree -- you are referring to the likelihood of the alignment with respect to the tree, right? I'm thinking that different alignments are not comparable using phylogenetic likelihoods because different alignment tools will produce alignments of ...
written 2.1 years ago by db5340
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Comparing sequence alignments using phylogenetic likelihoods?
... Hello, I am currently considering different multiple sequence alignment (MSA) algorithms that I could use to generate an alignment. For the comparison of different alignments (i.e. produced from different tools), I have heard it said that phylogenetic likelihoods could be used to compare different ...
alignment written 2.1 years ago by db5340
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MSA following hmmalign/hmmsearch?
... Hello, My question is in regards to the hmmsearch/hmmalign commands of the HMMER program. As an output, both of these commands produce a sequence alignment with respect to the HMM that was used to query the sequence database. My question is, from the aligned domain sequences that can then be extrac ...
hmmer written 2.2 years ago by db5340

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