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392

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hmmsearch didn't work with nucleotide genome

genome nucleotide genome hmmer hmmsearch tool written 9 months ago by lbroetto • 0 • updated 9 months ago by Alex Reynolds ♦ 26k

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310

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Exact match with query architecture option for local version of HMMER

hmmsearch hmmer written 10 months ago by Sej Modha ♦ 3.9k

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2.1k

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Installation issues with hmmer2

hmmer2 hmmsearch prokka hmmer written 4.2 years ago by JV • 380 • updated 2.2 years ago by RamRS ♦ 19k

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706

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hmmsearch to show all sequences

multifasta hmmsearch hmmer written 2.5 years ago by srx3001 • 0

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803

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Problem with SMART

smart hmm hmmsearch error written 2.7 years ago by alejocn5 • 0

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1.1k

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Parsing Hmmsearch tblout format

hmmsearch written 3.4 years ago by aproposdiver • 10

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1.8k

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hmmer core dumps, does not create proper MSA Stockholm format files

phmmer hmmsearch hmmer written 3.7 years ago by kdiaz17 • 0 • updated 3.7 years ago by seanrobertseddy • 50

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1.3k

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biopython SearchIO with hmmearch 2 error

python hmmer hmmsearch biopython written 3.8 years ago by MAK • 10 • updated 3.8 years ago by Biostar ♦♦ 20

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Recent Replies

A: Extract number of SNPs for any given gene by Andrew Su ♦ 4.8k
You can get this info using the myvariant.info API. For example, suppose you are interested in S...
C: How do I use t-test for genes in R? by JC ♦ 7.0k
Even when you can do the test by yourself, it's better if you use the tools already implement for...
A: what is vdb_names in blastdb_aliastool by h.mon ♦ 22k
VDB is a database format to store "next-gen" sequencing data. See the handout [Using SRA Toolkit ...
C: psmc bootstrap plotting? by momccarthy.3 • 0
Hey I'm having this same problem, did you find a solution in the end? Cheers, Morgan
C: Identifying consensus sequence between multiple Arabidopsis genome sequences by bioinforesearchquestions • 190
Hi VKKodali, I am trying to find consensus between the full genome sequence not against the refer...
C: Bio.PDB parsing PDB file by RamRS ♦ 19k
> I thought Bio.PDB was automatically set up to get files from the PDB database I don't think...
C: Identifying consensus sequence between multiple Arabidopsis genome sequences by vkkodali • 700
NCBI has a few Arabidopsis genome assembly - assembly alignments [here](ftp://ftp.ncbi.nlm.nih.go...
C: Filtering fastq vs BAM for fragment size range by ATpoint ♦ 11k
Yeah, but I cannot answer this, as I never tried. I would always go for the after-alignment step ...
C: load/parse cwl using Java by pr80ik • 0
reported as [github issue][1] [1]: https://github.com/common-workflow-language/cwlavro/issues/16
C: Filtering fastq vs BAM for fragment size range by rbronste • 230
This is a nice approach thanks, I guess my question was moreso if the two approaches (before and ...
C: Filtering fastq vs BAM for fragment size range by ATpoint ♦ 11k
Simply try it. Given that you asked how to subset a BAM by TLEN in a previous thread, here is a p...
C: How to calculate significance, my tumors are enriched in the middle versus upper by ATpoint ♦ 11k
It is completely unclear what kind of data you have, what the experimental conditions are and wha...

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