Moderator: Steve Moss

gravatar for Steve Moss
Steve Moss2.2k
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Website:
https://www.gawbul.io/
Last seen:
7 months, 2 weeks ago
Joined:
7 years, 4 months ago
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Posts by Steve Moss

<prev • 227 results • page 1 of 23 • next >
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Answer: A: What Are The Exact Algorithms For Motif Discovery?
... Also worth checking out Biology Meets Programming: Bioinformatics for Beginners https://www.coursera.org/learn/bioinformatics which can help with learning the basics of the algorithms underpinning motif discovery. ...
written 10 months ago by Steve Moss2.2k
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Comment: C: Anyone Use Normd As A Quality Control For Msas
... The README has the following, so I assume it must be the latter? norMD Objective Function for multiple sequence alignments (version 1.3, Jan 2003) ...
written 10 months ago by Steve Moss2.2k
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Comment: C: Anyone Use Normd As A Quality Control For Msas
... I was just looking for this too, and managed to find norMD1_3.tar.gz after searching Google, however, the version I have, when compiled, returns: ./normd Version 1.2 Is this the same with your version Pierre? I wondered if they just hadn't incremented the version number in the source? ...
written 10 months ago by Steve Moss2.2k
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Comment: C: Looking For A Command Line Version Of Ncbi Taxonomy 'Stratification' Tool
... Which Python script? In my https://github.com/gawbul/bioinformatics-scripts repository? Could you submit an issue request on GitHub please? ...
written 3.0 years ago by Steve Moss2.2k
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Comment: C: Automatically Getting The Ncbi Taxonomy Id From The Genbank Identifier
... I modified your script slightly to retrieve these data for some accession IDs that I failed to recover when running blastdbcmd -entry_batch against my local blast database install, even though I could get information on them when using Entrez (my local data was the latest release from the FTP). I ra ...
written 4.1 years ago by Steve Moss2.2k
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Answer: A: Map Genbank Gi To Accession Numbers (A Million Times)
... You can also use: blastdbcmd -db dbname -entry_batch long_list_of_nucleotide_gi_numbers.txt -outfmt '%a %g' -logfile entry_batch_stdout.log This has the benefit of only outputting the sequences you are interested in, for further downstream analyses. Any failed queries will be kicked out to entry_ ...
written 4.1 years ago by Steve Moss2.2k
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Answer: A: Bio C++
... You could try Biological Sequence Analysis Using the SeqAn C++ Library here http://www.amazon.co.uk/Biological-Sequence-Analysis-Mathematical-Computational/dp/142007623X. ...
written 4.4 years ago by Steve Moss2.2k
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Comment: C: Delete A Node From Newick Tree
... Cool, Sphinx'd version of the BioPython tutorial phylogenetics chapter here http://www.bio-cloud.info/Biopython/en/ch12.html ...
written 4.4 years ago by Steve Moss2.2k
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Comment: C: Delete A Node From Newick Tree
... +1 for Bio::Phylo mention - much better package for working with trees in Perl! ...
written 4.4 years ago by Steve Moss2.2k
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Comment: C: Delete A Node From Newick Tree
... That's pretty rubbish! Can you not view the updated tree without writing to a new file? ...
written 4.4 years ago by Steve Moss2.2k

Latest awards to Steve Moss

Popular Question 9 months ago, created a question with more than 1,000 views. For What Are Your Requirements When Examining A Bioinformatics Related Phd Thesis?
Appreciated 9 months ago, created a post with more than 5 votes. For A: Bioinformatics On Google+ (Search, Plus Your World)
Popular Question 9 months ago, created a question with more than 1,000 views. For What Is Your Experience With Promoter Prediction Programs?
Good Answer 11 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Scholar 13 months ago, created an answer that has been accepted. For A: Looking For A Command Line Version Of Ncbi Taxonomy 'Stratification' Tool
Good Answer 13 months ago, created an answer that was upvoted at least 5 times. For A: Bioinformatics On Google+ (Search, Plus Your World)
Appreciated 13 months ago, created a post with more than 5 votes. For A: Bioinformatics On Google+ (Search, Plus Your World)
Popular Question 21 months ago, created a question with more than 1,000 views. For How Can I Unify Genome Data From Different Sources?
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Great Question 3.1 years ago, created a question with more than 5,000 views. For Best Way To Concatenate Columns In Multiple Csv Files Of Differing Row Lengths?
Teacher 3.2 years ago, created an answer with at least 3 up-votes. For A: Bioinformatics/Cheminformatics/Biology Games
Appreciated 3.5 years ago, created a post with more than 5 votes. For A: Best Way For A Beginner To Get Up To Speed On Unix Quickly?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For How Can I Unify Genome Data From Different Sources?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Is There Such A Thing As A Ucsc Api?
Popular Question 3.5 years ago, created a question with more than 1,000 views. For Getting All Exons From Ensembl...
Appreciated 3.7 years ago, created a post with more than 5 votes. For Is There Such A Thing As A Ucsc Api?
Appreciated 3.7 years ago, created a post with more than 5 votes. For What Are Your Requirements When Examining A Bioinformatics Related Phd Thesis?

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