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

mining of Expressed Sequence tags for Identification of

atP Binding cassette transporters in Human Brain

Sandeep Kumar vishwakarma 1, 2 , Syed ameer Basha Paspala 1, 2 and

aleem ahmed Khan 1, 2 *

1 Centre for Liver Research and Diagnostics, Deccan College of Medical Sciences,

Kanchanbagh, Hyderabad, Andhra Pradesh-5000 58, INDIA.

2 PAN Research Foundation, Narayanguda, Hyderabad, Andhra Pradesh, INDIA.

*Corresponding author: Aleem Ahmed Khan , aleem_a_khan@rediffmail.com

abstract

The general quality of expressed sequence tag (EST) sequences and the general

absence of positive selection in these sequences make ESTs an attractive tool for

the study of evolutionary relationship and sequence searches. Due to emerging

scope of ABC transporters in human brain diseases treatment investigations and

drug resistance, here we investigate the ABC transporter ESTs present in human

brain. 15 ESTs were identified and used for cluster generation to see the gaps

and subjected to phylogenetic analysis to identify the evolutionary relationship

and conserved structures. Investigation and clustering of human ESTs from brain

allows extension of data sampling from outside of the genome project.

Keywords: Expressed sequence tag, ABC transporters, cluster generation,

phylogenetic analysis.

Expressed sequence tag (EST) is short sub-sequence of a cDNA molecule and is

used to identify gene sequences, transcripts analysis and gene discovery (Adams

et al., 1991). Due to its wide applications in genomics identification of various

genes, investigation of ESTs has developed quickly, with 74,186,692 ESTs entered

in public databases for all organisms. Rapid identification of novel markers and

evolutionary relationship among human ESTs searches has improved since last

decades and now the highest dbEST is available for human on NCBI approximately

8,704,790 (GenBank, 1 st January 2013).

ESTs are generated from individual clones of cDNA library and results in a

relatively low quality fragment with limited length to approximately 500 to 800

nucleotides. Because these clones consist of DNA that is complementary to mRNA,

the ESTs represent portions of expressed genes. The current understanding of the

human set of genes includes the existence of thousands of genes based solely on