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SACS provides web interfaces to a number of sequence analysis tools. Those tools that require a minimum of supporting resources to function are open to the general public. Others requiring more support are reserved for the use of SACS subscribers.

 

Programs fall into these general areas

Database searching
BLAST
Alignments
pairwise and multiple alignment tools
EMBOSS
wEMBOSS interface to the entire EMBOSS package
and locally generated interfaces to selected EMBOSS programs
genome tools
various tools for looking at genome data
phylogenetics tools
various PHYLIP tools for looking at phylogenetic data
transmembrane protein TMD predictors and display
HMMTOP, Memsat, TMHMM and TOPO2


Database searching

sacs

BLAST

 
This page allows the user to do regular BLAST searches.
  Search locally the NCBI BLASTable databases and Uniprot's Swissprot and Trembl.  


Alignments

Pairwise alignments

needle

Uses the Needleman-Wunsch global alignment algorithm to find the optimum alignment (including gaps) of two sequences when considering their entire length.
public

stretcher

Needleman-Wunsch rapid global alignment of two sequences.
public

lalign

Lalign non-overlapping local alignment of two sequences.
public

matcher

Waterman-Eggert local alignment of two sequences.
public

water

Uses the Smith-Waterman algorithm (modified for speed enhancments) to calculate the local alignment.
public

Multiple alignments

ClustalW

Output from the Multiple Sequence Alignment program ClustalW(v1.8) can be color coded with mview for easier reading.
public

MultAlin

MultAlin, a Multiple Sequence Alignment tool designed by Florence Corpet, offers several comparison tables and has a gif output file which can be color coded.
public

muscle

A program for creating multiple alignments of amino acid or nucleotide sequences by R.C. Edgar that is faster than Clustalw.
public

t_coffee

A multiple sequence alignment program with many options.
public


EMBOSS Programs

wEMBOSS
Interface

wEMBOSS is a web interface to the EMBOSS software package for biological sequence analysis. wEMBOSS started as a coordinated effort from Martin Sarachu of the Argentinian EMBnet Node and Marc Colet from the Belgian EMBnet node.
sacs

remap

Display restriction enzyme binding sites in a nucleotide sequence.
public

transeq

Translate nucleic acid sequences.
public


genome tools

gene finding

A tool for finding the location of a gene on either the human or mouse genomes and then going on to see other genes in that neighborhood.
public

gene environments

A tool for comparing the gene locations across a number of species.
public


phylogenetics tools

drawtree

PHYLIP's drawtree program with preset font and postscript output.
no changes to font, label, or tree orientation possible
public
         

drawtree advanced

PHYLIP's drawtree program with user selectable values.
changes to font, label, or tree orientation possible
sacs
         

drawgram

PHYLIP's drawgram program with preset font and postscript output.
no changes to font, label, type or gram orientation possible
public
         

drawgram advanced

PHYLIP's drawgram program with user selectable values.
changes to font, label, type or gram orientation possible
sacs


Transmembrane Segment Prediction and display programs

HMMTOP

HMMTOP is a transmembrane prediction tool developed by G.E. Tusnady and I. Simon. TOPO2 displays the prediction.
public

Memsat

Memsat is a transmembrane prediction tool developed by David Jones. TOPO2 displays the prediction.
public

TMHMM

TMHMM is a transmembrane prediction tool developed by A. Krogh, B. Larsson, G. von Heijne, and E.L.L. Sonnhammer. TOPO2 displays the prediction.
public

TOPO2

Display the topology of a transmembrane protein.
public


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