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Tools

NOTE: all tools listed below are open source!
Graham Alvare's Protein molecular weight counter (Python source code)
A molecular weight counter written in Python. This molecular weight counter reads any number of FastA files and outputs the molecular weight of each sequence as a CSV spreadsheet (Tab-delimited), which can be read in Excel or OpenOffice.
To run, type: python gmwcalc.py filename.fsa > output.csv

You may also use this tool online
Protein FastA file:
Graham Alvare's Simple Tag Mapper (GenBank features version)
A simple tool, which reads two GenBank files and compares the locus tags based on their sequences. The tag mapper, then, maps the tags between files. The tags which do not map perfectly (map perfectly means 100% homology of all base pairs in each locus tag), are listed at the bottom of the file with the closest match listed and the number of base pairs that do match between the two locus tags. Please note that this file reads the features keys of GenBank files for the locus tags (e.g. NCBI or IMG files).

This module requires BioPython to read the GenBank files.
If you are using IMG files, please use the following command to first convert the files to BioPython compatible GenBank Files: Graham's IMG GB file fixer
Graham Alvare's Protein statistics counter (Python source code)
A protein statistics calculator, which calculates the molecular weight, number of amino acids, and chemical formula; and estimates the pI of proteins in a FastA file. The output of the program is tab-separted CSV data, which can be fed into Excel or OpenOffice. The algorithm used for pI estimation is from Lukasz Kozlowski's Isoelectric Point Calculator - http://isoelectric.ovh.org.

Contact info

Graham Alvare
Max Rady College of Medicine
University of Manitoba
Winnipeg, Manitoba
Canada R3E 0W2

E-Mail:
Webpage: http://home.cc.umanitoba.ca/~alvare