Replacement for much used GCG programs
Exchanging sequences between packages
|
In
WWW2GCG |
In
wEMBOSS |
|
getseq |
newseq |
|
fromfasta ,
tofasta fromembl ,
toembl from* , to* |
seqret (any EMBOSS
program that reads/writes sequences) |
Sequence editing, manipulation and display
|
In
WWW2GCG |
In
wEMBOSS |
|
fetch |
seqret |
|
seqed command delete command insert |
no complete
solution yet cutseq pasteseq |
|
lineup |
no good solution yet |
|
assemble |
union |
|
shuffle |
shuffleseq |
|
reverse |
revseq |
|
chopup |
no more needed as EMBOSS reads any format |
|
publish |
showseq, prettyseq |
Translation
|
In
WWW2GCG |
In
wEMBOSS |
|
translate |
transeq |
Sequence comparison and alignment
|
In
WWW2GCG |
In
wEMBOSS |
|
compare+dotplot
(default (window stringency)) compare+dotplot
(word=n) |
dotmatcher dottup |
|
gap |
needle, stretcher (for long sequences) |
|
bestfit |
water, matcher (for long sequences) |
|
pileup, clustal |
clustal |
|
pretty |
cons, showalign |
Keyword-based databank searching
|
In
WWW2GCG |
In
wEMBOSS |
|
names |
whichdb |
|
indexsearch |
indexsearch |
|
stringsearch
(mode A) stringsearch
(mode B) |
textsearch no good solution
yet but advantageously replaceable by indexsearch |
Sequence-based databank searching
|
In
WWW2GCG |
In
wEMBOSS |
|
blast |
blast |
|
psiblast |
psiblast |
|
fasta |
fasta |
Patterns and gene finding
|
In
WWW2GCG |
In
wEMBOSS |
|
findpatterns |
fuzznuc,
fuzztrans, fuzzprot NB: uses PROSITE syntax (not GCG) to define pattern |
|
motifs |
patmatmotifs NB: ps_scan searches also PROSITE profiles |
|
codonpreference |
syco, wobble |
Phylogeny
|
In
WWW2GCG |
In
wEMBOSS |
|
distances+growtree |
clustalnj or ednadist/eprotdist+eneighbor |
Mapping
|
In
WWW2GCG |
In
wEMBOSS |
|
map - with option "Find translationally silent potential restriction sites" |
remap, restrict silent |
|
Mapsort mapsort+plasmidmap |
restrict cirdna (only
partial solution : input file with Tick positions must
be created "manually") |
Protein analysis
|
In
WWW2GCG |
In
wEMBOSS |
|
pepplot, peptidestructure+plotstructure |
garnier, pepinfo, octanol, pepwindow |
Primer selection
|
In
WWW2GCG |
In
wEMBOSS |
|
prime |
eprimer3
(=Primer3) |
|
primepair, melttemp |
no good solution yet |
DNA fragment assembly
|
gelstart gelenter gelmerge gelassemble gelview geldiassemble |
no good solution yet in In wEMBOSS but well replaced by STADEN pregap4+gap4,
accessible through a X-window interface. Contact BEN for more information |