Vishwakarma et al.

EST evidence. In this respect, ESTs have become a tool to refine the predicted

transcripts for those genes, which leads to the prediction of their protein products

and ultimately their function (Christoffels et al., 2001; Skrabanek et al., 2001).

High-throughput analyses of ESTs often encounter several challenges such

as poor data management which makes it difficult to write programs that can

unambiguously determine that two EST libraries sequenced from the same tissue

(Campagne et al., 2006). Similarly, disease conditions for the tissue are not

annotated in a computationally friendly manner which needs further analysis for

tissue specific gene expression for several genes and transcription factors.

The present study describes identification of ATP-binding cassette (ABC)

transporters ESTs in human brain. This will assist to get an idea of the possible

sources for EST data resources and the bottlenecks in EST analysis. We also

provide significant tools to analyze their proven utility in different application

areas, the general methods and protocols being followed for EST analysis obtained

from dbEST on NCBI.

materials and methods

dbEST, TIGR and UniGene are the most useful resources for the identification

of raw and cluster data of ESTs of many organisms. dbEST is one of the largest

repository of EST database on NCBI.To initiate in silico analysis, the EST database

was searched for ABC transporter gene clusters expressed in human brain tissues

using dbEST on NCBI. The ESTs of all 49 known ABC transporter gene entries

were downloaded and only those originating from human brain tissues were

considered for analysis (Nagaraj et al., 2007).

EST Pre-Processing

Automatically generated ESTs remains in low quality containing higher error

rates with vector sequence contamination; hence, these undesired sequences were

deleted from ESTs to reduce the overall redundancy and to improve the efficacy

of further analysis. Using dbEST in our analysis is obvious as each cluster is

generated by combined information from GenBank mRNA database, UniGene

and electronically spliced genomic DNA which are clustered and cleaned from

vector sequence contamination.

EST Clustering

A total of 15 ESTs expressing in human brain tissues were identified from seven

reported ABC transporter gene families. Clustering of 15 identified ESTs for ABC

transporters was performed to collect the overlapped sequences from the same

transcript of a gene into a unique cluster to reduce the redundancy. All EST cluster

scores were identified and converted into bar graph to know the gaps and false

8

Int. J. Bioinformatics and Biological Sci.: v.2 n.1&2, p. 7-12. March & June 2014