User: Wayne

gravatar for Wayne
Wayne380
Reputation:
380
Status:
Trusted
Location:
Syracuse, NY, United States
Website:
http://proteopedia.org...
Twitter:
fomightez
Last seen:
2 days, 20 hours ago
Joined:
5 years, 10 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 11 months ago by Wayne380
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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 11 months ago by Wayne380
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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 2.0 years ago by Wayne380
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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 2.4 years ago by Wayne380
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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 2.4 years ago by Wayne380
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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 2.4 years ago by Wayne380
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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 2.4 years ago by Wayne380
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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 2.5 years ago by Wayne380
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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 2.6 years ago by Wayne380
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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 2.7 years ago by Wayne380

Latest awards to Wayne

Scholar 10 months ago, created an answer that has been accepted. For A: How to know that your RNA-seq is stranded or not?
Supporter 13 months ago, voted at least 25 times.
Good Answer 3.0 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 3.2 years ago, created a post with more than 5 votes. For C: Samtools View: Only Forward Or Reverse Strand
Teacher 3.4 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 4.0 years ago, created a post with more than 5 votes. For C: Samtools View: Only Forward Or Reverse Strand
Commentator 4.1 years ago, created a comment with at least 3 up-votes. For C: Samtools View: Only Forward Or Reverse Strand

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