User: Charles E. Grant

Reputation:
220
Status:
Trusted
Location:
Seattle
Website:
http://noble.gs.washin...
Last seen:
7 years, 5 months ago
Joined:
9 years, 6 months ago
Email:
c******@u.washington.edu

I'm a computer programmer in the laboratory of William Noble in the Genome Science Department of the University of Washington. My primary responsibility if the maintenance of MEME Suite.

Posts by Charles E. Grant

<prev • 14 results • page 1 of 2 • next >
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Comment: C: How To Interpret Gap Penalty For Sequence Alignment?
... Is this in the context of a particular alignment program or are thinking about sequence alignment in the abstract. ...
written 7.5 years ago by Charles E. Grant220
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Answer: A: Motif Annotation
... If you are talking about DNA motifs, take a look at GOMO. It's part of the MEME Suite. Your motifs have to be in MEME format. "GOMO will use the DNA binding motifs to find putative target genes and analyze their associated GO terms. A list of significant GO terms that can be linked to the given moti ...
written 7.5 years ago by Charles E. Grant220
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Comment: C: Hidden Markov Models Within Sequence Analysis -- Dispelling Misconceptions + Fix
... @delinquentme, with respect to question one: if you are talking about sequence alignment, the HMM isn't concerned with the different states of the sequence over evolutionary history, except for the assumption that the sequences have a common ancestor. Rather we're looking at how states change as we ...
written 7.9 years ago by Charles E. Grant220
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Comment: C: Hidden Markov Models Within Sequence Analysis -- Dispelling Misconceptions + Fix
... @delinquentme, as ih3 says you don't need an HMM if you are just piling up reads and throwing out ones with mis-matches. On the other had HMM are useful if want to start worrying about whether a mis-match between an assembled sequence and a reference genome is a SNP or a sequencing error. Is their s ...
written 7.9 years ago by Charles E. Grant220
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Comment: C: Hidden Markov Models Within Sequence Analysis -- Dispelling Misconceptions + Fix
... @deliquentme, are thinking of using HMM to align sequences? In that case the nucleotide labels in the sequences are the observed data, and the hidden states are whether that position represents an insertion, a deletion, or a substitution. ...
written 7.9 years ago by Charles E. Grant220
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Comment: C: Hidden Markov Models Within Sequence Analysis -- Dispelling Misconceptions + Fix
... @delinquentme I'd second the suggestion to be more specific about the application of HMM you are interested in understanding. Typically you are not using an HMM to predict nucleotides. As you point out we're observing the nucleotides from our sequencing experiments. The goal of a HMM to predictions ...
written 7.9 years ago by Charles E. Grant220
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Comment: C: Entice Biologists To Learn R
... @mmarchin, of course they're capable of learning R, it's just a question of whether it is the best use of their time or not. Most of the biologists I know have plenty on their plate keeping up with biology and wet lab technology. If you can show them that learning R will be a net savings of time for ...
written 7.9 years ago by Charles E. Grant220
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Comment: C: About Punnett Squares
... I've no idea, since I don't know anything about plink. If your question is really about the specific use of Punnett Squares in plink then you should edit your question to reflect that. ...
written 8.0 years ago by Charles E. Grant220
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Answer: A: About Punnett Squares
... The alleles in Punnett Squares represent a higher level of abstraction then a simple base change. They can represent just about any variation in a genome that is linked to a clear phenotype. They might represent a single base change, or they might represent insertions, deletions, inversions or copy ...
written 8.0 years ago by Charles E. Grant220
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Answer: A: How Can I Search A Set Of Special Tfbs On All Of Human Promoters?
... I'm not sure if you are looking for software to search for matches to motifs, or something more elaborate. There are several tools available for searching for matches to motifs: POSSUM STUBBS Regulatory Sequence Analysis Tools (RSAT). In particular take a look at their 'matrix-scan' tool. MEME S ...
written 8.2 years ago by Charles E. Grant220

Latest awards to Charles E. Grant

Autobiographer 7.4 years ago, has more than 80 characters in the information field of the user's profile.
Appreciated 8.0 years ago, created a post with more than 5 votes. For A: About Punnett Squares
Teacher 8.0 years ago, created an answer with at least 3 up-votes. For A: About Punnett Squares
Appreciated 8.9 years ago, created a post with more than 5 votes. For A: Best Resources To Learn Molecular Biology For A Computer Scientist.
Good Answer 8.9 years ago, created an answer that was upvoted at least 5 times. For A: Best Resources To Learn Molecular Biology For A Computer Scientist.
Teacher 8.9 years ago, created an answer with at least 3 up-votes. For A: Best Resources To Learn Molecular Biology For A Computer Scientist.

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