Thu Dec 01, 2022 21:18 pm


SRM Bioinformatics Tools


     SRM BIT(SRM Bioinformatics Tools) provides a collection of web based programs written in PERL-CGI to perform protein and nucleotide sequence analysis in efficient manner.

Pattern Finder
     Pattern matching helps to identify the position and frequency of the given pattern or motif or part of sequence. The pattern can be located in any sequence DNA, RNA and Protein. Patten Finder accepts normal pattern and/or regular expression patterns.

Repeat Finder
     Repeat Finder predicts the repeats (eg: TATATA) based on two criteria entered by user.

(i) Maximum repeat size. Eg. If the users want to predict dimer(AA) and trimer(AAA), then the user have to enter 3 as maximum repeat size value.
(ii) Minimum repeat occurrence value. Eg. (AG)2 - minimum occurrence is two i.e. AGAG.

Codon Usage
     Codon usage returns the frequency of each codon type. It represents the preference of an amino acid towards synonyms codon.

Sequence Statistics
     For DNA Sequence the following sequence statistics are computed.

(i) Nucleotide Base Count,
(ii) Molecular weight and
(iii) GC Content.

And for protein it computes

(i) Amino acid count: The frequency of individual amino acids.
(ii) Amino acid count based on properties: total numbers of amino acids are counted based on five properties. Hydrophobic, Hydrophilic, Aromatic, Aliphatic and Basic Amino Acids.
(iii) Molecular Weight.
(iv) Extinction Coefficient: It indicates how much light a protein absorbs at a certain wave length and
(v) Grand average of hydropathicity (GRAVY) which indicates the solubility of the protein.

Clustal W
     Performs multiple sequence alignment and provides the result in one of the four alignment options (GDE, Phylip, PIR and GCG).

Sequence Fragmenter
     The sequence fragmenter is used to get the subsequence from the original sequence. It provides an option to retrieve single or multiple subsequences based on start and stop positions.