User: Bill Pearson

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Bill Pearson860
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Posts by Bill Pearson

<prev • 41 results • page 1 of 5 • next >
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Answer: A: Check Conservation of a Given Protein Domain
... If the region you are interested in is the 40 amino-acid huntington domain linked above, then you can answer your question by going to Pfam (pfam.xfam.org) and looking up DUF3652 (or PF12372). That page has a link to the evolutionary tree for the domain [1]. If you are looking for a different reg ...
written 16 months ago by Bill Pearson860
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Answer: A: What kind of BLAST to use in Gene Ontology?
... You should use BLASTP. It will have fewer false positives and higher sensitivity. ...
written 16 months ago by Bill Pearson860
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Answer: A: How to create a tab delimited file?
... You do not need three "@group"s -- you either need three scalars ($field0, $field1, $field2) or one @group, which you could print with join("\t",@group); A simpler solution is to: while (my $line = <$input>) { chomp($line) print join("\t",split(/\s+/,$line),"\n" } or ...
written 16 months ago by Bill Pearson860 • updated 16 months ago by genomax85k
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Answer: A: Pfam alignments: full vs uniprot
... To answer your question directly, the HMM models parameters are based on alignments of the model to the 27 million proteins in the Uniprot reference proteomes. Your confusion probably comes from the fact that the most recent versions of Pfam have two different sets of tables for different sets of s ...
written 2.4 years ago by Bill Pearson860
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Answer: A: Make matrix of protein pairwise identities/similarities from multiple protein se
... Phylip uses its own special interleaved sequence alignment, which is definitely neither FASTA format nor CLUSTAL format, but you can find programs that will convert. Phylip format is well known and quite old (1980's). The advantage of Phylip's protdist over clustal's is that it gives corrected (sc ...
written 2.4 years ago by Bill Pearson860
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Answer: A: Python bioinformatics mini project ideas
... Here is a project that requires you to look up refseq protein sequences at NCBI, find their Uniprot accessions, determine whether the NCBI and Uniprot proteins are in fact identical, and then asks whether the proteins contain complete Pfam domains: https://fasta.bioch.virginia.edu/biol4230/labs/ac ...
written 2.4 years ago by Bill Pearson860
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Answer: A: Make matrix of protein pairwise identities/similarities from multiple protein se
... The Phylip program package (http://evolution.genetics.washington.edu/phylip/getme-new1.html), which uses an unfortunate format for multiple sequence alignment, includes "protdist", which does exactly what you want, and converts from observed distance to evolutionary distance. ...
written 2.4 years ago by Bill Pearson860
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Comment: C: Was FASTA ever popular?
... FASTP and FASTA (and I assume FASTQ, but I did not name it) are NOT acronyms. We picked "FAST" because our method was much faster than previous methods (at the time, we reduced search time from 24hr on a VAX750 to about 5 min), the P was for "protein", later A was for "All" (there was also a FASTN ...
written 2.7 years ago by Bill Pearson860
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Answer: A: downloading protein sequences
... Take a look at the slides in this link: [http://fasta.bioch.virginia.edu/biol4230/lects/biol4230_9_web_resources.pdf][1] Slides 4 - 7 show a general strategy for using NCBI's esearch/efetch sites to (1) look up the refseq protein accession for your genes using a search term (your gene name) and (2 ...
written 3.2 years ago by Bill Pearson860 • updated 3.2 years ago by genomax85k
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Answer: A: retro-engineered annotation on genome assembly
... A possible strategy: (1) blastp all of fungus1 vs fungus2 and vice versa. Find the proteins in fungus1 that do not have significant hits (possibly with a percent identity and coverage threshold) in fungus2, or have hits that only cover part of the protein, and vice-versa. (2) take the proteins in ...
written 3.7 years ago by Bill Pearson860

Latest awards to Bill Pearson

Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Was FASTA ever popular?
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For A: I Need To Plot 73 Mutations On A Large Gene With >60 Exons
Scholar 2.4 years ago, created an answer that has been accepted. For A: retro-engineered annotation on genome assembly
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: I Need To Plot 73 Mutations On A Large Gene With >60 Exons
Scholar 2.7 years ago, created an answer that has been accepted. For A: retro-engineered annotation on genome assembly
Scholar 3.2 years ago, created an answer that has been accepted. For A: retro-engineered annotation on genome assembly
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: I Need To Plot 73 Mutations On A Large Gene With >60 Exons
Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: I Need To Plot 73 Mutations On A Large Gene With >60 Exons
Commentator 3.8 years ago, created a comment with at least 3 up-votes. For C: Was FASTA ever popular?
Commentator 3.8 years ago, created a comment with at least 3 up-votes. For C: Was FASTA ever popular?
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: I Need To Plot 73 Mutations On A Large Gene With >60 Exons
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: How To Identify Proteins Present Only In Pathogens But Not In Non-Pathogens (Vir
Teacher 6.8 years ago, created an answer with at least 3 up-votes. For A: How To Reduce Fasta Output?
Teacher 8.3 years ago, created an answer with at least 3 up-votes. For A: How To Reduce Fasta Output?
Good Answer 8.3 years ago, created an answer that was upvoted at least 5 times. For A: Does Needlman-Wunsch Algorithm Works With Float Values In Similarity Matrix?
Teacher 8.3 years ago, created an answer with at least 3 up-votes. For A: Does Needlman-Wunsch Algorithm Works With Float Values In Similarity Matrix?
Teacher 8.4 years ago, created an answer with at least 3 up-votes. For A: Why The Default Expect Threshold In Pblast Is 10?
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Good Answer 8.4 years ago, created an answer that was upvoted at least 5 times. For A: Why The Default Expect Threshold In Pblast Is 10?

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