User: James Ashmore

gravatar for James Ashmore
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London
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5 years, 12 months ago
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6 years, 6 months ago
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Posts by James Ashmore

<prev • 23 results • page 2 of 3 • next >
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Comment: C: How Can I Efficiently Parse Hmmer Results To Find Listed Domains And Their Archi
... Hello again, my script is working as I wanted thanks to your input. My output is now a list of sequence names with their associated Pfam domains tab delimited and written as they occur across the sequence e.g. Seq1 PYRIN \t DEAD I was wondering if there was any high throughput method of anal ...
written 6.5 years ago by James Ashmore90
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Comment: C: How Can I Efficiently Parse Hmmer Results To Find Listed Domains And Their Archi
... I thought as much, thanks a lot :) ...
written 6.5 years ago by James Ashmore90
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Comment: C: How Can I Efficiently Parse Hmmer Results To Find Listed Domains And Their Archi
... Hi neilfws, I managed to get the Biopython Hmmer parser working. I can print out the query sequence name, and a list of domain hits for that query. However, in one example I have two domains which are both above the inclusion threshold and greatly overlap. How would I go about extracting the domain ...
written 6.5 years ago by James Ashmore90
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Comment: C: How Can I Efficiently Parse Hmmer Results To Find Listed Domains And Their Archi
... More details would be really helpful, thank you! A sample of how it works in a Python script would also be great. ...
written 6.5 years ago by James Ashmore90
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How Can I Efficiently Parse Hmmer Results To Find Listed Domains And Their Architecture?
... I am running hmmscan on a fasta file containing a proteome using Pfam-A.hmm. I would like to parse the output from this scan to collect a list of domains identified in my sequences, as well as list any novel domain architectures which may have been identified. Currently I am parsing the output file ...
hmmer parser written 6.5 years ago by James Ashmore90 • updated 6.5 years ago by Travis Wheeler80
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Comment: C: How Do You Characterize Unknown Protein Sequences?
... The data is from the recently published proteome and transcriptome of the salamander N. viridescens. The measures taken to ensure they were protein-coding are substantial, involving proteomic validation by mass spec. Here are links to the two papers if you think anything may have been overlooked 1) ...
written 6.5 years ago by James Ashmore90
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Comment: C: How Do You Characterize Unknown Protein Sequences?
... Hi Jordan, yes these are protein sequences from the salamander species N. viridescens, the transcriptome of which has only recently been produced. There were around 600 protein-coding transcripts that did not show any hits in the NCBI databases (BLAST searches) and around 300 which showed hits to ur ...
written 6.5 years ago by James Ashmore90
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How Do You Characterize Unknown Protein Sequences?
... Hello, I have around 400 protein sequences which have no sequence similarity, no identifiable protein domains and no identifiable motifs. What steps should I take in order to characterize these proteins, both in function and strucure? My initial thoughts were as follows: 1) Compute physiochemical p ...
modeling sequence protein written 6.5 years ago by James Ashmore90 • updated 5.0 years ago by 5heikki8.6k
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Comment: C: Is There A Query Parameter For The Online Blast That Would Filter For Hits That
... Your second method seems much easier to understand and I'll have to implement something like that in the future, currently I've ended up writing a script which will take the gi number from the blast hit description, convert this to the taxon ID and retrieve the full lineage of the blast hit. There i ...
written 6.5 years ago by James Ashmore90
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Comment: C: Is There A Query Parameter For The Online Blast That Would Filter For Hits That
... Hi Peter, The method you suggest would retrieve hits from the caudata taxon only, however I want to retrieve hits from all taxons and filter for queries (not hits) which only have hits in the caudata taxon - i.e. unique caudata genes. My goal is to take the salamander transcriptome and see which tr ...
written 6.6 years ago by James Ashmore90

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