Categories

Archives

A sample text widget

Etiam pulvinar consectetur dolor sed malesuada. Ut convallis euismod dolor nec pretium. Nunc ut tristique massa.

Nam sodales mi vitae dolor ullamcorper et vulputate enim accumsan. Morbi orci magna, tincidunt vitae molestie nec, molestie at mi. Nulla nulla lorem, suscipit in posuere in, interdum non magna.

NCBI : Activity Personal BLAST Database Development ; Dylan Storey

Introduction/Background:

In order to compare previously sequenced RFLP clones and EST clones used in marker development for genetic mapping in pepper to a chip developed by industry a BLAST database of proprietary sequences needs to be compiled. Using the toolkit developed by NCBI I’m in currently in the process of compiling a database of these sequences. After that database is ready, a series of sequences from RFLP clones that have been historically used for mapping will be compared to sequences on the chip. It is my hope that high sequence homology will exist between RFLP sequence and data points on the chip, if ¬†high sequence homology does exist and linkage data also backs up the homology then the ability to call them orthologous will exist. With the declaration of these loci as orthologs comparisons between data from older southern based experiments to newer chip based experiments will be available. Because the sequence information from industry is proprietary I am unable to provide links to it.

Links to information / data repositories :

Database development

http://www.ncbi.nlm.nih.gov/staff/tao/URLAPI/unix_setup.html#2

RFLP clone sequences and linkage information:

http://sgn.cornell.edu/

EST sequence information:

Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome,Hyun-Jin Kim et al.,BMC Plant Biology 2008, 8:101 doi:10.1186/1471-2229-8-101

Questions:

Are previously used and reported marker systems orthologous to marker systems currently in development and use.

Comments are closed.