EMBOSS Open Software Suite

• wossname is your first to go command to search for all the tools

wossname "sequence alignment"

• total of around 100 tools, including data retrivel from web (fastq-dump)
• install EMBOSS: sudo apt-get install emboss
• You may need libx11-dev module (visualisation of graphs) sudo apt-get install libx11-dev
• Web based Version

Tools included (selection):

prophet gapped alignment

water smith waterman local alignment

infoseq get information of a sequence

showfeat get features of a seq, coils, bindingsites etc.

eprimer3 or primer3, primers and hybridization oligos, best one

water is highly accurate alignment but very slow

seqret fetches sequences from databases

getorf finds open reading frames

transseq translate nucleotides seq to proteins

dottup dot plot of pairwise alignment good image for publication

needle global alignment

prettyplot multiple seq. alignment and graphics

equicktandem microsatellites, palindroms, repeats

wEMBOSS

• you need a EMBOSS server (own or a other available somewhere (like a workstation))
• you access this with wEMBOSS
• all results can be created in html
• wEMBOSS needs to know if DNA or Protein sequence, then it shows associated programs
• GUI is user friendly but less flexible
• program shows you the associated "command line