Bioinformatics

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BIOINFORMATICS

PURIFICACION, MARYNOLD V.
CHEM 161.1 3L
2nd Semester AY 2012-1013

GROUPMATES:
Donato, Lualhati M.
Diaz, Manuelle Marie C.

Date Submitted: March 8, 2013

Laboratory Instructor: Ms. Herra Grajo

I. INTRODUCTION

Bioinformatics is the branch of biological science which deals with the study of methods for storing, retrieving and analyzing biological data, such as nucleic acid (DNA/RNA) and protein sequence, structure, function, pathways and genetic interactions. It is very important since it contains large amount of information regarding biomolecules that a human mind is not able to store and process such data. There are different data bases that can be used like National Center for Biotechnology Information (NCBI), European Molecular Biology Laboratory-European Bioinformatics Institute database (EMBL-EBI), GenBank (US-based), SwissProt/UniProt, DNA Data Bank of Japan (DDBJ), Entrez and PubMed. Basic Local Alignment Search Tool, or BLAST, is an algorithm for associating primary biological sequence information, like amino-acid sequences of various proteins or the nucleotides of DNA sequences. A BLAST search allows a researcher to compare a query sequence with a library or database of sequences, and identify library sequences that resemble the query sequence above a certain threshold. The BLAST program was designed by Stephen Altschul, Warren Gish, Webb Miller, Eugene Myers, and David J. Lipman at the NIH and was published in the Journal of Molecular Biology in 1990. On the other hand,ProtParam is a very useful softwarethat can compute various physico-chemical properties from a protein sequence. The parameters that can be computed by ProtParam include the molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity (GRAVY).

At the end of this exercise, the student should be able to understand the concept and process of bioinformatics; to know the process on how to use computer programs related in biological information; and to apply these programs on different protein sequences and identify different informations using these programs.

II. METHODOLOGY

The FASTA sequence of the given proteins namely; Myk, Gi, Glean, Astara, Niko, SR, Joma, Melai, Danne, Jay, Annie and Hani were analyzed using BLAST and ProtParam. BLAST showed the protein with that given sequence and its function was researched. ProtParam, on the other hand, showed the amino acid composition of the given protein, its theoretical IpH, estimated molecular weight and other pertinent information.

III. RESULTS AND DISCUSSION

Bioinformatics is the branch of biological science which deals with the study of methods for storing, retrieving and analyzing biological data, such as nucleic acid (DNA/RNA) and protein sequence, structure, function, pathways and genetic interactions. In this exercise, the computer program called Basic Local Alignment Search Tool (BLAST) was used to identify different protein sequences and determine the function of these proteins. Also, a computer program named ProtParam was used to determine the IpH and estimated molecular weight of the said proteins.

Different sequences of proteins were analyzed using these 2 algorithms to study their identities, properties and purposes. Table 1 show the list of the given protein sequences, their identity, their theoretical IpH and estimated molecular weight. The FASTA sequences of the different codes are also shown below.

PROTEIN SEQUENCES:
Myk
qavlslyasgrttgivldsgdgvthtvpiyegfalphailrldlagrdltdalmkiltergysftttaereivrdikeklayvaldyeqelesa Gi
mftasqegdgmskshvhrsvwwswlvgvltvvglglglgsgvglapgsaapsglaldrfadrplapidps Glean
mmvawwslflyglqvaapalaatpadwrsqsiyflltdrfartdgsttatcntadqkycggtwqgiidkldyiqgmgftaiwitpvtar Astara...
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