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Has anyone found an easy way to combine results from a comprehensive sequence search on several databases (CA, USGene, GQPAT, Geneseq) and several vendors (STN, Genomequest)? I'm putting together both a Word report and a Bizint chart, but there's a lot of manual data cleanup involved. When I was only doing one of these infrequently, it was doable, but now with a dozen to do in a month, I'm looking for a less time consuming process.
Any advice?
Comments (3)
Jun 24, 2009
A.J. D'Ambra says:
Hi Monica - Do you have a good text editor? I've used KEDIT (http://www.kedit.c...Hi Monica - Do you have a good text editor? I've used KEDIT (http://www.kedit.com/) and now I'm using UltraEdit (http://www.ultraedit.com/index.html). Both are text editors that allow editing in columns or blocks (like sequences) and with regular expressions, commands, and macros for routine tasks (like post-processing data from diverse sources). You can use them to clean up text in before importing into BizInt (we had to do this before BizInt revised its WPI/STN import filter to add the PIA field in the BIB format a few years back). KEDIT is simpler to use than UltraEdit (I'm still trying to figure out the macro language), but UltraEdit is on Novartis's standard apps list, so I'm stuck with it. Tom Wolff and most of the IR&A group at Exxon are seasoned pros on KEDIT. Tom and Sandra Unger each published an article on using KEDIT several years ago (find the links on http://www.wolffinfo.com/publications.htm).
Jun 24, 2009
Roy Zimmermann says:
Monica, another freeware editor which I've used for a few years now is Crimson E...Monica, another freeware editor which I've used for a few years now is Crimson Editor, well suited for find & replace operations, comparing lists of patent numbers, supports macros, etc. It's a small download, memory unintensive, unlike WORD or WORDPAD. I've had open up to 20 text files simultaneously in Crimson Editor. If you are permitted to obtain and install freeware or shareware, I'd recommend using Tucows.com or Shareware.com as the sources, since both have a sustained track records of virus checking installables.
Roy Zimmermann
Medtronic
Jun 29, 2009
Adrienne Shanler says:
Monica, For years, I have been merging BLAST data from STN, Genomequest, the in...Monica,
For years, I have been merging BLAST data from STN, Genomequest, the internet, GCG, etc. The average sequence search took about 2 hrs. to edit from a merging all the data into a text file to the final, organized Excel spreadsheet. It requires a good text editor. I use the Brief keymap in Codewright which uses keystroke macros. You don't have to learn to write programs for macros. Slickedit may do the same thing. If I can be of assistance, please contact me.
Adrienne