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MS&T cDNA Resource Center Commercial Website

Image courtesy of 3DScience.com

Forward / Reverse Alignment -

A simple alignment algarythm is used to align a "forward" and a "reverse" sequence and the concensus sequence is them outputed into a popup window.This scriptlet can be used to align two "5' to 3'" sequences or one with the reverse compliment of the second. Multiple sequencing reads can be aligned stepwise to complete the entire sequence for a template that required greater than two reads to complete.

Also included in the ouput is a "Strength of Match" - the size of the overlap between the two sequences. This overlap is what was used to create the "full" version.

Written by Adam Martin

Other Usefull Links
GPCR Database
Poland Thermal Profile
Translate DNA

Chang Bioscience Links
Reverse Complement
Restriction Digestion

Sequence Adjustment -

A quick scriptlet that takes an inputed sequence and allows you to perform multiple adjustments to a new outputed sequence. Those options include the Reverse, Compliment, Reverse Compliment, and a simple Clean up. The output can be formated in multiple ways including 80nt lines, 10nt blocks, etc...

Written by Adam Martin

Restriction Digest Analysis -

This scriptlet allows you to take an inputed sequence and easily visualize which restriction enzyme sites can be found within it. Currently it only has options for the common restriction sites found in pcDNA3.1+ from Invitrogen but those sites are also frequently found in other commercial sub-cloning vectors. Other common sites may be added in the future if the need arises.

Written by Adam Martin

Open Reading Frame (ORF) Finder -

This scriptlet takes an inputed sequence (with our without a name) in fasta format and outputs the first open reading frame (ORF) it finds within that sequence. Error checking tells you if there was no ATG start codon and/or if there was no stop codon found within frame.
A drop down menu lets you check the reverse compliment for a ORF as well- either way the ORF is displayed in the forward (5' to 3') orientation.

Written by Adam Martin

Quick GC Content -

This scriptlet takes an inputed sequence and analyses it for GC content and then visually displays the output in a popup window. Two hedgemarks are used within the graph to seperate moderate from extremely GC rich regions of the sequence. Two options are available for visualization: Full and Abbreviated, the ladder of which steps through 5nt's at a time. This option is faster but is sometimes slightly harder to "read".

Written by Adam Martin

Please contact Adam Martin (amartin@umr.edu) if you find errors or have questions/comments about any of the programs written by him on this page.