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BIOINFORMATICS

The document contains an assignment for a bioinformatics course. It includes short questions about k-tuple methods, bit scores, and e-values. It also describes the GOR secondary structure prediction algorithm, which uses probability parameters to predict protein secondary structure. Finally, it defines a motif as a significant sequence pattern and notes MEME server analyzes DNA/protein sequences to find motifs.

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ritesh singh
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49 views2 pages

BIOINFORMATICS

The document contains an assignment for a bioinformatics course. It includes short questions about k-tuple methods, bit scores, and e-values. It also describes the GOR secondary structure prediction algorithm, which uses probability parameters to predict protein secondary structure. Finally, it defines a motif as a significant sequence pattern and notes MEME server analyzes DNA/protein sequences to find motifs.

Uploaded by

ritesh singh
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© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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ASSIGNMENT: 02

NAME: SUBHI SINGH


ROLL NO: MBT/10019/19
SUBJECT: BIOINFORMATICS
BIOTECHNOLOGY DEPARTMENT
BIRLA INSTITUTE OF TECHNOLOGY MESRA, RANCHI.

1) Write short note on:


 K-tuple = Word method, also known as k-tuple methods, are heuristic methods that
are not guaranteed to find an optimal alignment solution, but are significantly more
efficient than Smith-Waterman algorithm from the word methods are best known for
their implementation in the database search tools FASTA and the BLAST family.
 Bit score = A bit score is another prominent statistical indicator used in addition to the
Evalue in a BLAST output. The bit score measures sequence similarity independent
of query sequence length and database size and is normalized based on the raw
pairwise alignment score.
 E-value =E-value is a parameter that describes the number of hits one can ‘’expect’’
to see by chance when searching a database of a particular size. It decreases
exponentially as the score (S) of the match increases. Essentially, the E-value is the
random background noise.

2) Describe the secondary structure prediction algorithm (GOR method).


 The GOR method (Garnier-OsguthorpeRobson) is an information theory based
method for the prediction of secondary structure in proteins. It was developed in
the late 1970s shortly after the simpler Chou-Fasman method, the GOR method is
based on probability parameters derived from empirical studies by X-ray
crystallography. However, unlike Chou-Fasman, the GOR method takes into
account not only the propensities of individual amino acids to form particular
secondary structures, but also the conditional probability of the amino acid to
form a secondary structure given that its immediate neighbors have already
formed that structure. The method is therefore essentially Bayesian in its analysis.

3) What do you mean by Motif, Describe the working principle of MEME server.
 Motif is a nucleotide or amino-acid sequence pattern that is widespread and has
been proved or assumed to have a biological significance.
 The working principle of MEME server are:
ASSIGNMENT: 02
NAME: SUBHI SINGH
ROLL NO: MBT/10019/19
SUBJECT: BIOINFORMATICS
BIOTECHNOLOGY DEPARTMENT
BIRLA INSTITUTE OF TECHNOLOGY MESRA, RANCHI.

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