BYU Library has also created a resource page of
Sequence Databases
Other DNA Sequencing Facilities
Tools
Sequence Tools on the Web:
Click on the links below in order to access the Sequencing Tools.
The Sequence Manipulation Suite - A collection of 30 different utilities for analyzing and manipulation sequence data.As seen in BioTechniques 28(6): 1102-1104.
A fairly complete list of proteomics tools maintained by
ExPASy (Swiss Institute of Bioinformatics).
Database Searching and File Manipulation
EMBL Tools - Database Searching, Browsing and Analysis Tools.
BLAST to FASTA Format - Will convert NCBI BLAST output to FASTA Format.
DNA Tools
WebCutter - will produce a restriction map of a sequence you input.
Open Reading Frame Finder - identifies all open reading frames using the standard or alternative codes.
Biological Online Collaboration -
multiple users can work together online on biological tasks.
Sanger Institute Software Solutions - many tools for manipulating DNA sequence.
Sequence Alignment
ESPript 3 - Tool to print a multiple alignment.
Multiple Sequence Alignment - At EBI.
Blast - align two sequences using BLAST
LALIGN - find multiple matching subsegments in two sequences
RNA Tools
mfold - RNA Secondary Structure Prediction.
RNAfold - Predict RNA secondary structure from sequence
Primers & Primer Design
Primer 3 - Picks PCR primers from nucleotide sequences you supply.
OligoCalc - Will calculate the T
M of your oligonucleotides.
Primer Analysis Software - NetPrimer and Beacon Designer free link.
Protein Tools
DNA to Protein Translator - Converts DNA sequences to protein sequences.
Peptide Property Calculator - Calculates Molecular Weight, Length of the Peptide, and Others.
Protein Calculator - Will calculate Molecular Weight, Charge, UV Absorbtion, Atom and Residue Counts, and Solvent Content.
PredictProtein - Prediction of transmembrane helix location and topology (Columbia University).
Miscellaneous
Centrifuge Helper - Helps to calculate g-values for various centrifuge models and rotors.
FreeWare Sequence Editing Software: (Download and install on your machine). Note: Please DO NOT install these software packages on DNASC computers.
There are many free programs available that can open .ab1 files, such as 4Peaks
(Mac), SnapGene Viewer
(Mac/PC), FinchTV
(Mac/PC), Sequence Scanner
(PC), and Chromas
(PC).
Sequence Analysis Software:
ClustalW2 - Multiple Sequence Alignment Program.
PHYLIP v3.57 - by Joe Felsenstein.
PAUP* v4.0 - by David Swofford.
TFPGA - Tools for Population Genetic Analyses, by Mark Miller.