Description of the Brugia malayi Database of Clustered ESTs

Generation of Database

The Brugia Database was generated by aligning 15032 Brugia sequences contained in dbEST as of September 18, 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 15032 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 Brugia consensus database contains 5541 consensus sequences, 4081 of which are singletons. 14 different cDNA libraries were used as templates for sequencing.

• Distribution of ESTs from each cDNA library in those Brugia consensus sequence clusters containing two or more ESTs.

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.

• Families/Processing from a blastn comparison of the Consensus database against itself to identify potential gene families, mRNA processing differences or cDNA cloning artifacts.
• GBNR Neighbors from a blastx search of gbnr to identify sequence similarities between the Toxo consensus sequences and the non-redundant genbank database.
• dbEST Neighbors from a blastn search of dbEST to identify related dbEST sequences.
• Motifs Summary from a motifs analysis (Prosite release 15) of the predicted peptides.
  Note: The phosphorylation sites and an amidation site were removed for this analysis.

Questions and complaints to brunkb@cbil.humgen.upenn.edu
Contents by Brian Brunk.