User: Torst

gravatar for Torst
Torst860
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

<prev • 94 results • page 1 of 10 • next >
0
votes
0
answers
584
views
0
answers
(Closed) Minia 2.0.3 binary spits out lots of HDF5 errors if -out-dir doesn't exit
... 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 ...
minia written 21 months ago by Torst860
0
votes
1
answer
620
views
1
answer
minia 2.0.3 problem building from source - hdf5/hdf5.h missing?
... 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 ...
minia written 21 months ago by Torst860 • updated 21 months ago by Rayan Chikhi1.2k
0
votes
1
answer
823
views
1
answers
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 Torst860
6
votes
1
answer
4.3k
views
1
answers
Answer: A: New To Bioinformatics, What Is A 6-Mer When It Comes To Alignment Algorithms (An
... 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 Torst860
0
votes
0
answers
1.7k
views
0
answers
Comment: C: Things to do with the clustered groups of proteins from orthoMCL tool???
... 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 Torst860
0
votes
2
answers
1.8k
views
2
answers
Answer: A: Identify restriction sites of a cDNA sequence using a dictionary
... 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 Torst860
0
votes
1
answer
1.3k
views
1
answers
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 Torst860
2
votes
2
answers
12k
views
2
answers
Comment: C: What Is A .Ptt File And How It Is Created?
... 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 Torst860
1
vote
1
answer
755
views
1
answers
Answer: A: Is It Possible To Use Blast+ To Hit Embl Database?
... 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 Torst860
0
votes
1
answer
871
views
1
answers
Answer: A: Problem Updating GO Gene Association Files with CVS
... Probably simpler to mirror the FTP site: ftp://ftp.geneontology.org/pub/go/gene-associations/   ...
written 3.4 years ago by Torst860

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
Appreciated 2.6 years ago, created a post with more than 5 votes. 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: 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?
Appreciated 3.1 years ago, created a post with more than 5 votes. For A: Blast Can'T Find Databases
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?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1873 users visited in the last hour