User: Wayne

gravatar for Wayne
Wayne330
Reputation:
330
Status:
Trusted
Location:
Syracuse, NY, United States
Website:
http://proteopedia.org...
Twitter:
fomightez
Last seen:
1 week ago
Joined:
4 years, 11 months ago
Email:
f********@gmail.com

fomightez on github

Posts by Wayne

<prev • 25 results • page 1 of 3 • next >
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Answer: A: How to remove a substring from each line using python 3
... Python 3: In case someone ends up here given the 'Python 3' portion of the OP's question: Without a regular expression: output = "" for line in input: if "[db_xref=Ensembl" in line: split_on_tag = line.split("[db_xref=Ensembl") output += split_on_tag[0] + ...
written 4 weeks ago by Wayne330
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Answer: A: Any tool that aligns sequences that use degenerated nucleotide coding
... The letters that PatMatch patterns allow match the IUPAC ambiguity codes as well. See the syntax nicely represented at [the Saccharomyces Genome Database's PatMatch tool portal](https://www.yeastgenome.org/nph-patmatch#examples). For more about the tool and various places to use it, I have a summar ...
written 4 weeks ago by Wayne330
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Comment: C: How To Find The Locations Of A Short Specific Sequence In A Genome With 1 Or 2 M
... @chahat_u PatMatch definitely isn't limited to Arabidopsis. Look at the other post I pointed at [here](https://www.biostars.org/p/209383/#313223). There are several web sites offering PatMatch working as a web tool for quite a few organisms beyond Arabidopsis. I list the ones I could find [here](htt ...
written 14 months ago by Wayne330
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Comment: C: Convert binding site formats from different databases and compare the motifs - a
... Looks like R. Taylor Raborn has something for the Homer motif to MEME format direction. His gist [here][1] includes [motif2meme.R][2] . I don't know if that is an older form of another one I see--> [MoVRs_Motif2meme.R][3]. (They are clearly related.) That MoVR repo also contains [MoVRs_Consensus2 ...
written 18 months ago by Wayne330
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Comment: C: How To Find The Locations Of A Short Specific Sequence In A Genome With 1 Or 2 M
... [PatMatch][1] allows controlling the number of mismatches and whether that includes insertions, deletions, and/or substitutions. There is a stand-alone version of the software available as posted about [here][2] in response to a related question. (In fact, at the [referenced resource][3] you can run ...
written 18 months ago by Wayne330
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Comment: C: find positions of a short sequence in a genome
... As pointed out [here][1], [PatMatch][2] has been offered a while on the web sites of several genomes. But there is also a stand-alone, command line-based version of the software described in the article that works with any FASTA file to find matches to sequence patterns. Find a list of the genomes o ...
written 18 months ago by Wayne330
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Comment: C: Program For Motif Search
... If anyone is looking to do this outside Arabidopsis on any sequence, you can use the stand-alone PatMatch described in the original article as well. I have set up a repo where you can launch an active Jupyter notebook system where it works via Binder at [https://github.com/fomightez/patmatch-binder] ...
written 18 months ago by Wayne330
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Comment: C: find positions of a short sequence in a genome
... +1 to igor for pointing out need to consider both strands. And +1 to Alex Reynolds for bringing up overlap/match stradling ends. I fleshed it more [here](https://github.com/fomightez/sequencework/tree/master/FindSequence). ...
written 20 months ago by Wayne330
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Comment: C: Single gene circos plot possible?
... I would think something like you can see at [Let’s Plot 3: Base pair resolution NGS (exome) coverage plots - Part 1](http://davemcg.github.io/post/let-s-plot-3-base-pair-resolution-ngs-exome-coverage-plots-part-1/) is what Devon or Frank was suggesting? ...
written 21 months ago by Wayne330
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Comment: C: Bioconductor package history
... You were on to something about visibility. In fact, Biostars does come up higher than Bioconductor support when searching for similar information and I found Martin Morgan's answer on Biostars [here](https://www.biostars.org/p/121699/#121721) to be quite informative and have links related to what I ...
written 22 months ago by Wayne330

Latest awards to Wayne

Supporter 11 weeks ago, voted at least 25 times.
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: How to know that your RNA-seq is stranded or not?
Appreciated 2.3 years ago, created a post with more than 5 votes. For C: Samtools View: Only Forward Or Reverse Strand
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: How to know that your RNA-seq is stranded or not?
Appreciated 3.1 years ago, created a post with more than 5 votes. For C: Samtools View: Only Forward Or Reverse Strand
Commentator 3.3 years ago, created a comment with at least 3 up-votes. For C: Samtools View: Only Forward Or Reverse Strand

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