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Search: Posts Made By: LeightonP
Forum: Bioinformatics 07-09-2015, 11:02 PM
Replies: 1
Views: 1,944
Posted By LeightonP
There are a number of options open to you. One of...

There are a number of options open to you. One of which is to use code that others have written and tested (always a decent first option!). BIGSdb may be useful for you...
Forum: Bioinformatics 03-20-2015, 04:03 AM
Replies: 7
Views: 5,982
Posted By LeightonP
You can count the number of blank lines in a file...

You can count the number of blank lines in a file (filename) with:


grep -c "^$" filename


or, if you consider whitespace to be "blank":


grep -c "^\s*$" filename
Forum: Bioinformatics 03-20-2015, 03:54 AM
Replies: 7
Views: 5,982
Posted By LeightonP
One of the frustrations of bioinformatics is that...

One of the frustrations of bioinformatics is that datasets don't always contain exactly what you expect. Did you check that there are - as you expect - no empty sequences?

I can reproduce your...
Forum: Bioinformatics 03-19-2015, 02:04 PM
Replies: 7
Views: 5,982
Posted By LeightonP
I would expect that the problem is that one of...

I would expect that the problem is that one of your sequences has no residues in it, but I can't reproduce the problem with your test data:


lpritc@Totoro:~$ more test.fas
>CBLN1|mouse|Q9R171...
Forum: Bioinformatics 10-29-2014, 12:19 PM
Replies: 4
Views: 1,862
Posted By LeightonP
It's a common task, so you might find that...

It's a common task, so you might find that someone has already written a tool/script that would suit your purposes, in a language that suits your workflow. There's also a tool in the galaxy toolshed...
Forum: Bioinformatics 10-29-2014, 12:11 AM
Replies: 4
Views: 1,862
Posted By LeightonP
Generally, you need to compare all strains with...

Generally, you need to compare all strains with all other strains. You only have reciprocal BLAST hits between two strains A and B if the BLAST has been performed reciprocally: A vs B, and B vs A.
...
Forum: Bioinformatics 05-29-2014, 11:02 PM
Replies: 1
Views: 1,206
Posted By LeightonP
Command-line options are processed by different...

Command-line options are processed by different libraries on OSX and your Linux distro. The OSX libraries are more particular about option (things that begin with a hyphen, e.g. -b0) placement.
...
Forum: Bioinformatics 04-16-2014, 11:43 PM
Replies: 7
Views: 4,988
Posted By LeightonP
If the aligned region contains only matches, then...

If the aligned region contains only matches, then the report of 100% identity for the aligned region will be correct.



Whether you should rely on E-value depends on your biological question. It...
Forum: Bioinformatics 12-12-2013, 08:24 AM
Replies: 3
Views: 4,757
Posted By LeightonP
Your best option then is to download the...

Your best option then is to download the sequences from that model organism, and use makeblastdb to construct a BLAST database from them.

You can find the makeblastdb documentation here:...
Forum: Bioinformatics 12-10-2013, 01:29 PM
Replies: 11
Views: 3,952
Posted By LeightonP
You might want to consider the pysam module:...

You might want to consider the pysam module: http://wwwfgu.anat.ox.ac.uk/~andreas/documentation/samtools/api.html and https://code.google.com/p/pysam/

(EDIT: I see Devon already suggested this -...
Forum: Bioinformatics 11-13-2013, 10:59 AM
Replies: 7
Views: 2,014
Posted By LeightonP
We didn't manage to close any of 25 bacterial...

We didn't manage to close any of 25 bacterial genomes with 454 only. I haven't used PacBio, but I hear good things about it for closing.
Forum: Bioinformatics 11-13-2013, 10:55 AM
Replies: 4
Views: 1,509
Posted By LeightonP
There's a download link on each individual page:...

There's a download link on each individual page: "Download KGML" - 4th from the left on the first page I linked to.

If you're abiding by the terms of the KEGG API, then you probably shouldn't bulk...
Forum: Bioinformatics 11-12-2013, 08:01 AM
Replies: 4
Views: 1,509
Posted By LeightonP
KEGG is a good place to get KEGG pathways ;) ...

KEGG is a good place to get KEGG pathways ;)

http://www.genome.jp/kegg-bin/show_pathway?org_name=ssc&mapno=00061&mapscale=&show_description=show

is a link for fatty acid biosynthesis in Sus...
Forum: Bioinformatics 11-07-2013, 03:24 AM
Replies: 4
Views: 7,006
Posted By LeightonP
If you can get your sequences into R, then the...

If you can get your sequences into R, then the oligonucleotideFrequency function (which underlies alphabetFrequency/dinucleotideFrequency etc.) may be helpful to you.
...
Forum: Bioinformatics 09-28-2013, 02:37 PM
Replies: 11
Views: 4,495
Posted By LeightonP
It's pretty straightforward ;) 1) Make sure...

It's pretty straightforward ;)

1) Make sure SignalP is installed and working on your system.
2) Run the script.

run_signalp.py [-o|--outfilename <output file>] <euk|gram+|gram-><FASTAfile>
...
Forum: Bioinformatics 09-28-2013, 01:40 AM
Replies: 11
Views: 4,495
Posted By LeightonP
One option is to wrap SignalP (and companion...

One option is to wrap SignalP (and companion programs) in a script that splits files for input, and concatenates output from several runs, e.g.

run_signalp.py...
Forum: Bioinformatics 09-19-2013, 06:58 AM
Replies: 1
Views: 1,253
Posted By LeightonP
Biopython has a Chromosome module for drawing the...

Biopython has a Chromosome module for drawing the basic shapes with annotation:

http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc277

but for the lines connecting markers, you might...
Forum: Bioinformatics 09-08-2013, 02:12 PM
Replies: 4
Views: 6,581
Posted By LeightonP
Biopython has a graphics library with a module...

Biopython has a graphics library with a module specifically for drawing chromosomes, which might be useful: http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc277
Forum: Bioinformatics 09-07-2013, 08:30 AM
Replies: 4
Views: 4,468
Posted By LeightonP
Or Biopython's GenomeDiagram...

Or Biopython's GenomeDiagram (http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc262) - you can get some quite complex images out of it:
...
Forum: Bioinformatics 01-04-2013, 02:56 PM
Replies: 6
Views: 3,096
Posted By LeightonP
An easy way to get the sequence is to ask...

An easy way to get the sequence is to ask entrez.efetch() to return a FASTA formatted sequence, as described in the Biopython tutorial at http://biopython.org/DIST/docs/tutorial/Tutorial.html#htoc55...
Forum: Bioinformatics 09-14-2012, 01:07 PM
Replies: 3
Views: 4,464
Posted By LeightonP
The KEGG FTP site is no longer free. The...

The KEGG FTP site is no longer free. The orthology database is part of the 'genes' subdirectory (link (http://www.kegg.jp/kegg/download/Readme/README.genes)) and - I believe - is only available by...
Forum: Bioinformatics 09-03-2012, 08:36 AM
Replies: 11
Views: 3,260
Posted By LeightonP
If you mean the cRBH algorithm, it's in the...

If you mean the cRBH algorithm, it's in the methods section.
Forum: Bioinformatics 09-02-2012, 11:31 PM
Replies: 11
Views: 3,260
Posted By LeightonP
I'm sure the OP finds your criticism of my...

I'm sure the OP finds your criticism of my writing style most helpful ;)
Forum: Bioinformatics 09-02-2012, 02:35 PM
Replies: 11
Views: 3,260
Posted By LeightonP
Not so much that it's only useful for detecting...

Not so much that it's only useful for detecting single-copy orthologues, but that



(from further into the paper)



Clearly they mean "all algorithms tested in this study", not "all...
Forum: Bioinformatics 09-02-2012, 11:38 AM
Replies: 11
Views: 3,260
Posted By LeightonP
It's worth noting though that, despite the name,...

It's worth noting though that, despite the name, OrthoMCL isn't necessarily the most reliable way to determine putative orthologues. From the OrthoMCL site:



i.e. there is MCL-based clustering...
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