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 8 months 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 9 months 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 9 months 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 9 months 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 9 months 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 9 months 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 12 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 13 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 3.2 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 3.2 years ago by cryptogenomicon80

Latest awards to cryptogenomicon

Scholar 9 months ago, created an answer that has been accepted. For A: Conflicting consensus sequences from different tools (bug in hmmemit?)
Teacher 9 months 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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