Comparison of the current RefSeq, Ensembl and EST databases for counting genes and gene discovery.

Abstract:

:Large amounts of refined sequence material in the form of predicted, curated and annotated genes and expressed sequences tags (ESTs) have recently been added to the NCBI databases. We matched the transcript-sequences of RefSeq, Ensembl and dbEST in an attempt to provide an updated overview of how many unique human genes can be found. The results indicate that there are about 25000 unique genes in the union of RefSeq and Ensembl with 12-18% and 8-13% of the genes in each set unique to the other set, respectively. About 20% of all genes had splice variants. There are a considerable number of ESTs (2200000) that do not match the identified genes and we used an in-house pipeline to identify 22 novel genes from Genscan predictions that have considerable EST coverage. The study provides an insight into the current status of human gene catalogues and shows that considerable refinement of methods and datasets is needed to come to a conclusive gene count.

journal_name

FEBS Lett

journal_title

FEBS letters

authors

Larsson TP,Murray CG,Hill T,Fredriksson R,Schiöth HB

doi

10.1016/j.febslet.2004.12.046

keywords:

subject

Has Abstract

pub_date

2005-01-31 00:00:00

pages

690-8

issue

3

eissn

0014-5793

issn

1873-3468

pii

S0014-5793(04)01596-0

journal_volume

579

pub_type

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