Hi Indranil, Different annotation sets will usually show differing numbers of genes. This is due to the fact that different methods are used to produce the gene sets. The number of items in the RefSeq track depends on the number of genes annotated in Genbank that align to the genome. In general, RefSeq tends to be a more restrictive set, thus the lower number you pointed out.
RefSeq's methods, for example: "RefSeq RNAs were aligned against the chicken genome using blat; those with an alignment of less than 15% were discarded. When a single RNA aligned in multiple places, the alignment having the highest base identity was identified. Only alignments having a base identity level within 0.1% of the best and at least 96% base identity with the genomic sequence were kept." In the genome browser, click on the track titles to see the track descriptions (incl. methods). Please let us know if you have any additional questions: [email protected] - Greg On 7/25/11 5:35 AM, Indranil Sinha wrote: > Hi, > Recently I have downloaded some of the files from the Chiken genome > (galGal3). I am using the "refflat.txt" file which is located at database > section. In this file only 5469 genes are present. I was wondering if this is > a complete list or not. When I tried to search some other Chicken database I > came to know that more than 14 thousand genes are present in the genome. > Thanks for your help. > > Kind Regards, > Indranil. > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
