Description of the Plasmodium falciparum Database of Clustered ESTs


Generation of Database

The Plasmodium Database was generated by aligning 2872 Plasmodium sequences contained in dbEST as of February 5, 1998. These sequences were first sorted by length, PolyA tracts trimmed and regions from both the 5' and the 3' end containing greater than 25% N's were removed. Sequences of less than 20 bp were eliminated resulting in 2872 sequences. These sequences were aligned using the cap2 program (Xiaoqiu Huang, 1996, Genomics 33, 21-31). This output file was then parsed to generate the files containing a library of consensus sequences and the clustering information.

Description of the Database

The Plasmodium consensus database contains 2260 consensus sequences, 1848 of which are singletons. 4 different cDNA libraries were used as templates for sequencing.

Analyses of the Database

A number of analyses were done to attempt to assign relatedness or function to the consensus sequences. These analyses are presented here in text form. The files are quite large and are better accessed by using a text search or via the individual sequences which are linked from within the database when information is available.

Questions and complaints to
Contents by Brian Brunk.