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Search: Posts Made By: malachig
Forum: General 07-09-2017, 03:36 PM
Replies: 10
Views: 11,503
Posted By malachig
I'm not sure I follow. It doesn't...

I'm not sure I follow. It doesn't reverse-complement the "regular expression" it reverse complements the restriction enzyme sequence (a string) that is used in the regular expression. We can either...
Forum: Bioinformatics 10-14-2013, 03:24 PM
Replies: 0
Views: 1,543
Posted By malachig
DGIdb: Mining the Druggable Genome

The druggable genome can be defined as the genes or gene products that are known or predicted to interact with drugs, ideally with a therapeutic benefit to patients. We developed the Drug Gene...
Forum: Bioinformatics 01-09-2013, 08:07 AM
Replies: 15
Views: 7,450
Posted By malachig
It looks like nilshomer's initial question was...

It looks like nilshomer's initial question was never addressed. We have the same concern with using this software:

"Looks like the license is fairly restrictive. Any chance of moving this to an...
Forum: Bioinformatics 12-07-2011, 07:38 AM
Replies: 13
Views: 10,663
Posted By malachig
Yes, you can define arbitrary numbers of pairwise...

Yes, you can define arbitrary numbers of pairwise and groupwise comparisons in any combination.

e.g.

Tumor #1 vs. Normal #1 (pairwise)
All Tumors vs. All Normals (groupwise)
Myc Amplified...
Forum: Bioinformatics 09-15-2011, 10:46 AM
Replies: 19
Views: 10,502
Posted By malachig
The ALEXA-seq...

The ALEXA-seq (http://www.ncbi.nlm.nih.gov/pubmed/20835245) and Trans-ABySS (http://www.ncbi.nlm.nih.gov/pubmed/20935650) manuscripts discuss the implications of intronic mapping reads for measuring...
Forum: RNA Sequencing 09-14-2011, 08:18 AM
Replies: 3
Views: 3,513
Posted By malachig
Other methods/tools related to the topic include:...

Other methods/tools related to the topic include:
ALEXA-seq (http://www.ncbi.nlm.nih.gov/pubmed/20835245)
Scripture (http://www.ncbi.nlm.nih.gov/pubmed/20436462)
Trans-ABySS...
Forum: Bioinformatics 08-16-2011, 05:56 AM
Replies: 5
Views: 4,172
Posted By malachig
kmcarr makes some good suggestions. More...

kmcarr makes some good suggestions.

More options:

Splign (http://www.ncbi.nlm.nih.gov/sutils/splign/splign.cgi)
Spidey (http://www.ncbi.nlm.nih.gov/spidey/)

If you look at a Refseq record...
Forum: Bioinformatics 06-27-2011, 04:13 PM
Replies: 30
Views: 10,375
Posted By malachig
I would also suggest you update to 0.4.2. The...

I would also suggest you update to 0.4.2. The way these things are specified in the config file have changed slightly. The new example may be more clear. After you have tried that, if you are...
Forum: Introductions 05-19-2011, 08:24 PM
Replies: 2
Views: 1,569
Posted By malachig
Welcome to the wonderful world of bioinformatics...

Welcome to the wonderful world of bioinformatics zhacker.

Many of the questions you ask have probably been answered elsewhere in SeqAnswers. As you search the forums you will also learn many...
Forum: Bioinformatics 05-19-2011, 07:07 PM
Replies: 13
Views: 10,663
Posted By malachig
Tools for detecting alternative splicing events

In addition to MISO and Cufflinks, ALEXA-seq (http://www.alexaplatform.org/alexa_seq/) is another tool that focuses on analysis at the feature level (exon, exon-exon junction, intron, etc.). The...
Forum: Bioinformatics 11-19-2010, 11:17 AM
Replies: 9
Views: 1,623
Posted By malachig
Regarding the comment that the observation may...

Regarding the comment that the observation may simply be due to biology. Good point! Once you convince yourself that the observation is not due to an artifact of the analysis (mapability, small...
Forum: Bioinformatics 11-19-2010, 10:41 AM
Replies: 9
Views: 1,623
Posted By malachig
Tophat/cufflinks does try to predict novel exons...

Tophat/cufflinks does try to predict novel exons and junctions. I'm not sure how well it handles small exons... Mapping small reads to the genome and then trying to find small exons is a...
Forum: RNA Sequencing 11-17-2010, 11:13 PM
Replies: 23
Views: 8,445
Posted By malachig
Yeah, I would agree with that. It really...

Yeah, I would agree with that. It really invaluable to have a few decent boxes (high memory ones even better) that have access to all the same storage mounts as the cluster nodes themselves...
Forum: RNA Sequencing 11-17-2010, 02:15 PM
Replies: 23
Views: 8,445
Posted By malachig
Yes, and its not the only problematic name i have...

Yes, and its not the only problematic name i have seen in use in the forums. I guess we should avoid such usernames and/or avoid using them in the text of post replies so that they do not pollute...
Forum: General 11-17-2010, 02:00 PM
Replies: 10
Views: 11,503
Posted By malachig
In case you feel that my previous post was...

In case you feel that my previous post was dodging your question :) ... attached is an example Perl script that you could use as a starting point. It uses regex to identify occurrences of one...
Forum: General 11-17-2010, 01:19 PM
Replies: 10
Views: 11,503
Posted By malachig
This should be fun. A real classic...

This should be fun. A real classic bioinformatics task for beginners.

There are some good books out there for learning how to solve these problems.
Beginning Perl for Bioinformatics...
Forum: Bioinformatics 11-17-2010, 11:53 AM
Replies: 9
Views: 1,623
Posted By malachig
I agree with mgogol. One possible explanation is...

I agree with mgogol. One possible explanation is mapping, although with 50mers you would think some part of the gene would be mappable. How big is this gene? How many exons?

Try a BLAT of some...
Forum: RNA Sequencing 11-17-2010, 11:39 AM
Replies: 23
Views: 8,445
Posted By malachig
Our cluster uses Sun Grid Engine (sge). ...

Our cluster uses Sun Grid Engine (sge). Submitting jobs to the cluster is accomplished using a wrapper for the 'qsub' utility of sge. Basically the submission command is just pointing to a batch...
Forum: Bioinformatics 11-16-2010, 09:22 PM
Replies: 5
Views: 4,921
Posted By malachig
Hello hanifk, Welcome to the wonderful...

Hello hanifk,

Welcome to the wonderful world of RNA-seq analysis. :).

RNA-seq can have very good signal-to-noise ratios compared to other expression analysis methods (e.g. microarrays). ...
Forum: RNA Sequencing 11-16-2010, 04:52 PM
Replies: 6
Views: 8,361
Posted By malachig
For added convenience to people landing here ......

For added convenience to people landing here ... in Griffith et al. Nature Methods. 2010 Oct;7(10):843-847 [Abstract...
Forum: General 11-16-2010, 04:08 PM
Replies: 10
Views: 6,576
Posted By malachig
Just noticed an alternative tool that might serve...

Just noticed an alternative tool that might serve the same function as wise2 for this problem called 'ProSplign (http://www.ncbi.nlm.nih.gov/sutils/static/prosplign/prosplign.html)' that has recently...
Forum: Bioinformatics 11-16-2010, 01:20 AM
Replies: 3
Views: 1,401
Posted By malachig
It seems like the next-gen, fast, short read...

It seems like the next-gen, fast, short read aligners are generally focused on aligning entire reads and do not do substring alignments. You may be stuck using an old school aligner. BLAST...
Forum: Bioinformatics 11-16-2010, 01:03 AM
Replies: 7
Views: 3,368
Posted By malachig
I believe assembled size includes the size of...

I believe assembled size includes the size of known gaps in the genome assembly. The sequenced size does not include the size of these gaps. Using physical mapping of a genome (e.g. BAC library...
Forum: Bioinformatics 11-16-2010, 12:40 AM
Replies: 3
Views: 1,859
Posted By malachig
If your goal is simply to identify reads that...

If your goal is simply to identify reads that look like repeats and remove them from downstream analysis ... you could download a suitable set of repeat element sequences from RepBase...
Forum: RNA Sequencing 11-04-2010, 07:38 PM
Replies: 3
Views: 12,619
Posted By malachig
Hello BioR, Welcome to the field of...

Hello BioR,

Welcome to the field of bioinformatics! Our own member 'MDY' wrote such a tutorial here (http://seqanswers.com/forums/showthread.php?t=7068).

My next piece of advice is to keep...
Showing results 1 to 25 of 116

 


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