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@ 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:
| 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
