i have downloaded gene2accession from the ncbi ftp site with the intention of extracting out chromosome start and stop points for mouse genes. many genes are annotated with multiple positions. for example 11287 has 6 different positions. i know there is some uncertainty with these annotations, but i had no idea how many multiple positions are actually assigned to individual entrez gene ids. how do annbuilder and biomart determine which is the "best" to use? if i want to build my own annotation tables from ncbi, is there a better table to download than gene2accession, i.e. something with a one-to- one correspondence between genes and chromosomal positions? thanks, mark -- --- Mark W. Kimpel MD ** Neuroinformatics ** Dept. of Psychiatry Indiana University School of Medicine 15032 Hunter Court, Westfield, IN 46074 (317) 490-5129 Work, & Mobile & VoiceMail (317) 663-0513 Home (no voice mail please)

Hi, Mark, AnnBuilder retrieves chromosome location data from UCSC Genome Browser. You can query UCSC Genome Browser directly or download data from http://hgdownload.cse.ucsc.edu/downloads.html biomart (BioMart and biomaRt) queries data from Ensembl (along with other databases). There are some collaborations between Ensembl and UCSC. I am sure others on the list can help you out on this part. best nianhua