User: cryptogenomicon

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Posts by cryptogenomicon

<prev • 10 results • page 1 of 1 • next >
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Comment: C: E-value results from hmmsearch are not accurate. [HMMER]
... I agree with that. Looks like the input is a random alignment. The title of the question is misleading. ...
written 5 weeks ago by cryptogenomicon80
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Comment: C: HMMER: Failed to open target sequence database for reading
... Pfam-A.fasta is a FASTA sequence file. It is not a profile HMM database. (Have you looked at it? If not, look at it.) ...
written 11 weeks ago by cryptogenomicon80
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Comment: C: HMMER: Failed to open target sequence database for reading
... hmmpress is for HMM files that you're going to search with hmmscan; not for FASTA files that'll be searched with phmmer. ...
written 11 weeks ago by cryptogenomicon80
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Comment: C: Conflicting consensus sequences from different tools (bug in hmmemit?)
... hmmemit will only output canonical residues (20 aa or 4 nt). ...
written 11 weeks ago by cryptogenomicon80
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Answer: A: HMMER: Failed to open target sequence database for reading
... It means that your file `HMMER/database/Pfam-A.fasta` can't be opened for reading. It either doesn't exist, or you don't have read permission for it. Also, if you are trying to search a protein sequence against Pfam, you generally want to be using hmmscan or hmmsearch, not phmmer. phmmer is for sea ...
written 11 weeks ago by cryptogenomicon80
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Answer: A: Conflicting consensus sequences from different tools (bug in hmmemit?)
... Because hmmemit is emitting the maximum likelihood sequence, according to the profile HMM's parameterization. ("majority-rule" in hmmemit means w.r.t. the profile HMM, not w.r.t. the MSA that the HMM was built from. hmmemit takes the HMM as input, not the MSA.) ...
written 12 weeks ago by cryptogenomicon80
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Comment: C: How to generate a multiple HMM file with HMMER?
... Yes, you can simply concatenate HMMER profile HMM files. ...
written 5 months ago by cryptogenomicon80
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Answer: A: Does hmmsearch look at the reverse complement of the fasta?
... hmmsearch doesn't, but nhmmer (which is meant for DNA/DNA comparison) does. Pretty sure this is documented, too. ...
written 6 months ago by cryptogenomicon80
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Answer: A: Don't get hits on HMMER
... I don't know what you mean by 3' slicing sequences (typo for the 3' splice site consensus?) but: HMMER is intended for identifying statistically significant sequence relationships, as a proxy for sequence homology -- i.e. comparison scores that you wouldn't expect to see by chance in a target seque ...
written 2.6 years ago by cryptogenomicon80
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Answer: A: Is there a way to perform a multiple sequence alignment in HMMER (hmmalign) usin
... hmmalign performs global alignments to your sequences, not local alignments. If you're trying to get hmmalign to align a complete sequence (containing domains A and B) to a profile of domain A, then the sequence of domain B will either be left as an overhang or misaligned, because there is nothing f ...
written 2.6 years ago by cryptogenomicon80

Latest awards to cryptogenomicon

Scholar 12 weeks ago, created an answer that has been accepted. For A: Conflicting consensus sequences from different tools (bug in hmmemit?)
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Conflicting consensus sequences from different tools (bug in hmmemit?)

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