@ uhura
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These EMBOSS web interfaces are currently available:

wEMBOSS: start session

W2H: start session

 

Jalview: A very nice multiple alignment editor with options for coloring etc.

The sequence analysis WiKi FAQ (frequently asked questions)

YSAP: Your Sequence Analysis Pipeline (PTA filtering and clustering of sequences)


These are all sorts of documentation links concerning EMBOSS:
 
link description
programs HTML description of each emboss program
quick guide A two page PDF summary of emboss
USA Description of the emboss Uniform Sequence Address
domainatrix A Word document describing domainatrix (protein domain tools)
emboss-gcg A Powerpoint presentation comparing emboss and GCG
emboss-interfaces A Powerpoint presentation describing the interfaces
emboss-talk A Powerpoint presentation about emboss

 

Essential EMBOSS applications:

(please note that sequence viewing and editing is inherent in the interfaces!)

application description
abiview display of sequencer trace files
ehmmbuild produces an HMM model from a set of aligned sequences
ehmmcalibrate calibrates an HMM (prior to ehmmsearch)
ehmmsearch searches with an HMM against a sequence database
emma multiple alignment (an interface to clustal)
eprimer3 primer calculation ("prime")
esim4 alignment of mRNA to gDNA
merger merge two overlapping sequences
needle global alignment of two sequences ("gap")
prettyplot nice viewing of multiple alignments
remap display sequence with restriction sites and translation
revseq reverses and complements a sequence ("reverse")
seqret sequence retrieval from databases ("fetch")
sixpack display sequence with 6-frame translation and ORFs
water local alignment of two sequences ("bestfit")
vectorstrip removal of vector from sequences
wossname keyword search for applications, e.g. wossname alignment


Additional sequence analysis software which is installed on uhura:
(command line access only)

Multiple Sequence Alignment
ClustalW 1.83 help
Probcons 1.09 doc syntax
Muscle 3.51 doc syntax

Phylogeny
Tree-Puzzle 5.2, maximum likelihood tree reconstruction, doc
PAML 3.14, maximul likelihood and Ks determination, doc
PHYLIP 3.65, a suite of phylogeny tools, doc

ORF/gene prediction
ESTScan 2.0b, ORF prediction doc paper masters thesis make your own matrix
FrameD 1.0, ORF prediction doc
Wise2, gene and ORF prediction, doc

Spliced alignment
MGalign 1.3.6, alignment of mRNA/cDNA to gDNA, syntax
GenomeThreader 0.9.46, tool for efficient, optimal spliced alignment of transcript and protein sequences to genomic sequences manual syntax
AAT package 1.52, spliced alignment of transcript and protein sequences to genomic sequences README
exonerate 1.0.0, a generic tool for sequence comparison which also allows spliced alignment of transcript and protein sequences to genomic sequences man page
splign 1.19, NCBI's utility for computing cDNA-to-Genomic, or spliced sequence alignments. online documentation
sim4 2003-09-21, align an expressed DNA sequence with a genomic sequence, allowing for introns (there is also an embassy version available: esim4)

Java TreeView helper scripts
helper (perl) scripts, for the Java TreeView software (e.g. used for heat maps from expression or taxonomic profiling), usage examples


Contact: stefan.rensing@biologie.uni-freiburg.de