User: Torst
Torst • 860
- Reputation:
- 860
- Status:
- Trusted
- Location:
- Australia
- Website:
- http://www.bioinformat...
- Last seen:
- 11 months, 2 weeks ago
- Joined:
- 5 years, 10 months ago
- Email:
- t**************@gmail.com
Microbial bioinformatics, *-omics.
Posts by Torst
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... This fails: rm -fr foo && ./minia -in ~/tmp/R1.fastq -out-dir foo
This works: mkdir foo && ./minia -in ~/tmp/R1.fastq -out-dir foo
If 'foo' doesn't exist it spits LOTS of messages like this:
HDF5-DIAG: Error detected in HDF5 (1.8.11) thread 0:
#000: /home/vagrant/gatb-tools/gat ...
written 21 months ago by
Torst • 860
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... Is this some issue with assumption of hdf5 library being installed at system level instead of using bundled one?
cd /tmp/minia20151207-2659-lh8xo7/minia-2.0.3-Source/build/ext/gatb-core/src && /bio/linuxbrew/bin/g++-5 -Os -w -pipe -march=core2 -I/tmp/minia20151207-2659-lh8xo7/minia-2.0.3-So ...
written 21 months ago by
Torst • 860
• updated
21 months ago by
Rayan Chikhi • 1.2k
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Answer:
A: net charge of my protein
... EMBOSS has a "pepstats" tool to do this:
http://emboss.bioinformatics.nl/cgi-bin/emboss/help/pepstats
You can do it online here:
http://emboss.bioinformatics.nl/cgi-bin/emboss/pepstats
...
written 3.2 years ago by
Torst • 860
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... A 6-mer is a subsequence of 6 letters (nucleotides or amino-acids).
For example, a length 10 DNA sequence has 5 possible 6-mers: the sequences using bases 1..6, 2..7, 3..8, 4..9, and 5..10. Think of a sliding window of length 6 moving across the sequence one letter at a time.
Aligning two sequenc ...
written 3.2 years ago by
Torst • 860
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... Be warned that OrthoMCL does not output the singleton clusters ie. some genes are unique.
Other tools you might want to consider are ProteinOrtho5 and kClust and cd-hit which can do similar things (and much faster).
...
written 3.2 years ago by
Torst • 860
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... You need to search for each recognition sequence string within the cDNA string.
In python you would use the find() method in the String object: http://www.tutorialspoint.com/python/string_find.htm
...
written 3.2 years ago by
Torst • 860
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Answer:
A: Blast output query
... In response to "2) In the tabular output, there is query sequence match start and end point as well as subject sequence start and end point. Which should I be using as a start and end point for sequence extraction? Query sequence or subject sequence?"
The "query" is the input file you specified wit ...
written 3.2 years ago by
Torst • 860
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... Yes, I wrote that module. There are still some tools that want a PTT file. They aren't much use for unfinished genomes, because they can only refer to ONE sequence at a time, so if you have 200 contigs, you need 200 PTT files....
...
written 3.2 years ago by
Torst • 860
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... It is possible you have been throttled by ENA for using the web service too much.
NCBI have explicit guidelines on this:
http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=DeveloperInfo
Do not overload the NCBI servers. If you are intending to perform more than 2 ...
written 3.4 years ago by
Torst • 860
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... Probably simpler to mirror the FTP site: ftp://ftp.geneontology.org/pub/go/gene-associations/
...
written 3.4 years ago by
Torst • 860
Latest awards to Torst
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Samtools / Bcftools Missing Random Obvious Single Base Indels
Good Answer
2.6 years ago,
created an answer that was upvoted at least 5 times.
For A: Blast Can'T Find Databases
Good Answer
2.6 years ago,
created an answer that was upvoted at least 5 times.
For A: How To Blast A Sequence Against Multiple Databases
Appreciated
3.1 years ago,
created a post with more than 5 votes.
For A: How To Blast A Nucleotide Profile (Pssm) Against A Nucleotide Database?
Teacher
3.1 years ago,
created an answer with at least 3 up-votes.
For A: K-Mer Correction In Rna-Seq Data For Transcriptome Assembly?
Supporter
3.4 years ago,
voted at least 25 times.
Student
3.9 years ago,
asked a question with at least 3 up-votes.
For Samtools / Bcftools Missing Random Obvious Single Base Indels
Teacher
4.0 years ago,
created an answer with at least 3 up-votes.
For A: How To Blast A Nucleotide Profile (Pssm) Against A Nucleotide Database?
Teacher
4.5 years ago,
created an answer with at least 3 up-votes.
For A: Visualization Of Sequencing Data From Bacteria (Prokaryotes)
Teacher
5.8 years ago,
created an answer with at least 3 up-votes.
For A: How To Blast A Sequence Against Multiple Databases
Teacher
5.9 years ago,
created an answer with at least 3 up-votes.
For A: Blast Can'T Find Databases
Teacher
5.9 years ago,
created an answer with at least 3 up-votes.
For A: K-Mer Correction In Rna-Seq Data For Transcriptome Assembly?
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