Comments for Biogeeks http://bio-geeks.com Wed, 18 Aug 2010 10:54:32 +0200 http://wordpress.org/?v=2.8.4 hourly 1 Comment on High throughput sequencing: Primer removal by Stinus http://bio-geeks.com/?p=261&cpage=1#comment-2393 Stinus Wed, 18 Aug 2010 10:54:32 +0000 http://bio-geeks.com/?p=261#comment-2393 Well, basically you simply need to make a pairwise alignment program that reads in pairs of reads, perform the alignment as described, and outputs the genomic part of each read in the pair. This should then iterate over the two fastq files containing your paired end reads and generate two new fastq files. Obviously, you need to keep track of the position in each file (as each read covers four lines), the id etc. but those are minor details. My own C++-program is not really what you would call user friendly at the moment. It is purely used in-house. Well, basically you simply need to make a pairwise alignment program that reads in pairs of reads, perform the alignment as described, and outputs the genomic part of each read in the pair. This should then iterate over the two fastq files containing your paired end reads and generate two new fastq files. Obviously, you need to keep track of the position in each file (as each read covers four lines), the id etc. but those are minor details. My own C++-program is not really what you would call user friendly at the moment. It is purely used in-house.

]]> Comment on High throughput sequencing: Primer removal by Peter Andrews http://bio-geeks.com/?p=261&cpage=1#comment-2367 Peter Andrews Tue, 17 Aug 2010 18:47:13 +0000 http://bio-geeks.com/?p=261#comment-2367 I do not understand how to readily translate the insights you made into code. Ideally I would want to be able to just pass in Illumina fastq sequence files and have all primer contamination removed so that I could then re-run the alignment in Bowtie. I do not understand how to readily translate the insights you made into code.

Ideally I would want to be able to just pass in Illumina fastq sequence files and have all primer contamination removed so that I could then re-run the alignment in Bowtie.

]]> Comment on Practical guide to microRNA target prediction by Raya Khanin http://bio-geeks.com/?p=643&cpage=1#comment-2085 Raya Khanin Sun, 08 Aug 2010 22:56:12 +0000 http://bio-geeks.com/?p=643#comment-2085 I just stumbled on your post while doing my research for a review I am currently working on. Good post but it will greatly benefit from a few updates. First of all, the down-regulating effect of microRNAs on protein translation has been experimentally confirmed in at least two high-throughput studies: Baek D, Villén J, Shin C, Camargo FD, Gygi SP, Bartel DP. Nature. 2008 Sep 4;455(7209):64-71. Epub 2008 Jul 30. The impact of microRNAs on protein output. Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N. Widespread changes in protein synthesis induced by microRNAs. Nature. 2008 Sep 4;455(7209):58-63. Epub 2008 Jul 30. Secondly, these two papers, as well as numerous others afterward, evaluated various target prediction algorithms on the proteomic data. Thirdly, PicTar allows for targets with imperfect seed matches that are highly conserved. It is quite plausible that new versions of other prediction methods refined their algorithms and now search for imperfect seeds as well (I have not been following closely recent developments in the field). Raya Khanin Bioinformatics Core MSKCC I just stumbled on your post while doing my research for a review
I am currently working on.

Good post but it will greatly benefit from a few updates.

First of all, the down-regulating effect of microRNAs on protein translation has been experimentally confirmed in at least two high-throughput studies:

Baek D, Villén J, Shin C, Camargo FD, Gygi SP, Bartel DP.
Nature. 2008 Sep 4;455(7209):64-71. Epub 2008 Jul 30.
The impact of microRNAs on protein output.

Selbach M, Schwanhäusser B, Thierfelder N, Fang Z, Khanin R, Rajewsky N.
Widespread changes in protein synthesis induced by microRNAs.
Nature. 2008 Sep 4;455(7209):58-63. Epub 2008 Jul 30.

Secondly, these two papers, as well as numerous others afterward, evaluated various target prediction algorithms on the proteomic data.

Thirdly, PicTar allows for targets with imperfect seed matches that are highly conserved. It is quite plausible that new versions of other prediction methods refined their algorithms and now search for imperfect seeds as well (I have not been following closely recent developments in the field).

Raya Khanin
Bioinformatics Core
MSKCC

]]> Comment on Wordpress plugin for listing Pubmed publications by Elfar http://bio-geeks.com/?p=541&cpage=1#comment-1566 Elfar Sat, 03 Jul 2010 07:40:44 +0000 http://bio-geeks.com/?p=541#comment-1566 Hi Ben, looks good, thanks for the info :) -elfar Hi Ben,

looks good, thanks for the info :)

-elfar

]]> Comment on Wordpress plugin for listing Pubmed publications by Ben http://bio-geeks.com/?p=541&cpage=1#comment-1558 Ben Fri, 02 Jul 2010 15:25:02 +0000 http://bio-geeks.com/?p=541#comment-1558 better way (sorry for spamming, but may be useful for other visitors .. $searchterm = '"' .get_the_author_meta('user_lastname') .',%20' . get_the_author_meta('user_firstname') . '"[Full%20Author%20Name]'; better way (sorry for spamming, but may be useful for other visitors ..

$searchterm = ‘”‘ .get_the_author_meta(’user_lastname’) .’,%20′ . get_the_author_meta(’user_firstname’) . ‘”[Full%20Author%20Name]‘;

]]> Comment on Wordpress plugin for listing Pubmed publications by Ben http://bio-geeks.com/?p=541&cpage=1#comment-1556 Ben Fri, 02 Jul 2010 15:01:10 +0000 http://bio-geeks.com/?p=541#comment-1556 oops, if you search for Full Name author, you should write the display name as Doe, John instead of John Doe :-) oops,

if you search for Full Name author, you should write the display name as
Doe, John
instead of John Doe
:-)

]]> Comment on Wordpress plugin for listing Pubmed publications by Ben http://bio-geeks.com/?p=541&cpage=1#comment-1555 Ben Fri, 02 Jul 2010 14:45:36 +0000 http://bio-geeks.com/?p=541#comment-1555 ok, this do the trick in the function.php of the module replace the initial $searchterm definition by this by $searchterm = '"' .strtr(get_the_author_meta('display_name'), " ", "%20") . '"[Full Author Name]'; and assign a display name as John doe , in the member profile and it works, unless you have a complete homonym in pubmed.. another thing is the possiiblity to limit the search to the last 5 papers by modifying the 200 to 5 in the dispmax= field regards, ben ok, this do the trick

in the function.php of the module
replace the initial $searchterm definition by this
by

$searchterm = ‘”‘ .strtr(get_the_author_meta(’display_name’), ” “, “%20″) . ‘”[Full Author Name]‘;

and assign a display name as John doe , in the member profile

and it works, unless you have a complete homonym in pubmed..

another thing is the possiiblity to limit the search to the last 5 papers by modifying the 200 to 5 in the dispmax= field

regards,
ben

]]> Comment on Wordpress plugin for listing Pubmed publications by Ben http://bio-geeks.com/?p=541&cpage=1#comment-1547 Ben Fri, 02 Jul 2010 12:54:55 +0000 http://bio-geeks.com/?p=541#comment-1547 yes, i understand that.. anyway, i'll give a short try, to see what's possible ;-) i'll let you know if i'm succeeding. benoit yes, i understand that.. anyway, i’ll give a short try, to see what’s possible ;-)

i’ll let you know if i’m succeeding.
benoit

]]> Comment on Wordpress plugin for listing Pubmed publications by elfar http://bio-geeks.com/?p=541&cpage=1#comment-1546 elfar Fri, 02 Jul 2010 12:41:05 +0000 http://bio-geeks.com/?p=541#comment-1546 Hi again, good to hear and thanks for the info. Let me know if I misunderstand, but I assume, you mean the author of the wordpress page so you can dynamically load the papers based on the guy who made the page. No that is not possible, although if there is some method in WP to call this it shouldn't be too complicated to add. But, the problem with this also, is that if you simply search by author name, there are not extremely names that are so unique (like my full name ;) ) so this would list a lot of papers not written by this author but guys with the same name as well, unless you specify some additional search criteria. -elfar Hi again,

good to hear and thanks for the info.

Let me know if I misunderstand, but I assume, you mean the author of the wordpress page so you can dynamically load the papers based on the guy who made the page. No that is not possible, although if there is some method in WP to call this it shouldn’t be too complicated to add. But, the problem with this also, is that if you simply search by author name, there are not extremely names that are so unique (like my full name ;) ) so this would list a lot of papers not written by this author but guys with the same name as well, unless you specify some additional search criteria.

-elfar

]]> Comment on Wordpress plugin for listing Pubmed publications by Ben http://bio-geeks.com/?p=541&cpage=1#comment-1545 Ben Fri, 02 Jul 2010 12:31:57 +0000 http://bio-geeks.com/?p=541#comment-1545 Hello, sorry for the trouble, but i was trying to use the plugin available in this page without success ; so i wanted to do it by myself. I've just tried to use the extension available on wordpress.com via the installation menu and it works well (call made with execphp! So, you can say it works with WP 3.0 ;) may i use your time again, about my last question: is it possible to call for the page's author name directly? because it's not possible through the admin page i think.. again, BRAVO ben Hello,

sorry for the trouble, but i was trying to use the plugin available in this page without success ; so i wanted to do it by myself.
I’ve just tried to use the extension available on wordpress.com via the installation menu and it works well (call made with execphp!
So, you can say it works with WP 3.0 ;)

may i use your time again, about my last question: is it possible to call for the page’s author name directly? because it’s not possible through the admin page i think..

again, BRAVO
ben

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