Reverse Complement

Reverse Complement

Reverse Complement is commonly used in Bioinformatics for various purposes. Here is the tool that does the job without much effort, there are simple Perl programs that could be run locally for the purpose. This tool is provided by GENE INFINITY, this can also do reverse and complementary separately. Hope this helps, the tool is located here, Reverse Complement

Protein Blast against another set of proteins

Protein Blast against another set of proteins

This tool is provided by NCBI/ BLAST/ blastp suite: BLASTP programs search protein databases using a protein query.This gives BLAST of a query protein against a set of other proteins. I found it useful when you don't wish to BLAST your query against whole protein database, instead a set of proteins given by the user. This tool is located here, Protein Blast against another set of proteins

PeptideCutter

PeptideCutter: http://expasy.org/tools/peptidecutter/

This tool is provided by ExPASy. This predicts potential cleavage sites cleaved by proteases or chemicals in a given protein sequence. 

PeptideCutter returns the query sequence with the possible cleavage sites mapped on it and /or a table of cleavage site positions. Single or multiple enzymes can be selected for the purpose. PeptideCutter

Predicting Antigenic Peptides

Predicting Antigenic Peptides

This is a program that predicts those segments from within a protein sequence that are likely to be antigenic by eliciting an antibody response. The method used here is the method of Kolaskar and Tongaonkar (1990). 

Predictions are based on a table that reflects the occurrence of amino acid residues in experimentally known segmental epitopes. Segments are only reported if the have a minimum size of 8 residues. The reported accuracy of method is about 75%. 

The program is located here Predicting Antigenic Peptides

Sequence analyzer

Sequence Massager: http://www.attotron.com/cybertory/analysis/seqMassager.htm

Nucleic Acid Sequence Massager is a very easy to use tool for convention of DNA to RNA, RNA to DNA, Upper Case to Lower Case and vice verse, Removal of FASTA format, Removal of HTML tags, Removal of number, White spaces, line breaks.

I find this tool very handy.