Department of Bioinformatics and Computational Biology

RefseqVerifier:Overview

From MD Anderson Bioinformatics
Jump to: navigation, search

RefSeq Verifier Web Site

Logo
RefSeq Verifier
Overview
Description This website provides a tool to perform RefSeq match for pairs of affy probe set and cDNA sequences that correspond to the same UniGene cluster by using blast search program 'bl2seq'.
URL http://bioinformatics.mdanderson.org/RefSeqVerifier/
Development Information
Current Version 1.0




Help and Support
Contact Kevin R. Coombes
Discussion Project Forum


For a given query file including UniGene ID, Affy probeset ID and GenBank accession number, this website provides a tool to perform RefSeq match for pairs of affy probe set and cDNA sequences that correspond to the same UniGene cluster by using blast search program 'bl2seq'.

For any question concerning QDA behind the scene, please contact Jiexin Zhang (jiexinzhang@mdanderson.org)

Contents


Corresponding publication

Yuan Ji, Kevin Coombes, Jiexin Zhang, Sijin Wen,James Mitchell, Lajos Pusztai, W. Fraser Symmans and Jing Wang.
RefSeq refinements of UniGene-based gene matching improve the correlation of expression measurements between two microarray platforms.
Applied Bioinformatics. 2006; 5(2): 89-98.

Documentation

About Query Input

Each row of queryfile contains UniGene ID, Affy probeset ID and GenBank accession number of the cDNA sequence, seperated by spaces.

Sample query file:

Hs.6111 202986_at AA019774
Hs.127686 216986_s_at AA825491
Hs.323443 213064_at T66840
Hs.166975 203380_x_at AA598965
Hs.112669 205883_at AA148548
Hs.401388 218122_s_at AA219198
Hs.439109 207152_at R52089
Hs.380684 222063_s_at R31300
Hs.365207 221544_s_at AA418545
Hs.23440 209285_s_at AA987446


Result Explanation

Unigene ID
UniGene cluster ID
RefSeq_ID
GenBank accession number of the RefSeq sequence
cDNA Access Number
GenBank accession number of the cDNA sequence
probe set ID
U133A probe set ID
cDNA iden
The number of identical base pairs in the alighment between cDNA and the RefSeq sequence
probe set iden 
The number of identical base pairs in the alignment between affy probe set and the RefSeq sequence
cDNA_distTo3
The number of base pairs from the end of alignment between cDNA and RefSeq to the 3' end of RefSeq "NA" if there is no significant similarity between cDNA and RefSeq
probeset_distTo3
The number of base pairs from the end of alignment between affy probe set and RefSeq to the 3' end of RefSeq. "NA" if there is no significant similarities between affy probeset and RefSeq
cDNA probeset
The number of identical base pairs in the alignment between cDNA and affy probe set sequence


Support

For Frequently Asked Questions, Bug Reports, and other concerns, please visit the forum at this link

Retrieved from "https://bcbweb.mdanderson.edu/main/RefseqVerifier:Overview"