OReilly sequence analysis in a nutshell a guide to common tools and databases jan 2003 ISBN 059600494x

[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
danprogram(EMBOSS)
dasycladaceancode
databases
BLAST,indexing
CPGISLE,producingentryformatreports
DNAsequence,searching
EMBOSS,searchingforsequenceswithspecifiedIDsornumbers
PRINTS
preprocessingforusewithPSCAN
PROSITEmotif
REBASE
predictingcutsitesinDNAsequences
searchingforrestrictionenzymes
sequences,tablelistingwaystoaccess
dbiblastprogram(EMBOSS)
dbifastaprogram(EMBOSS)
dbiflatprogram(EMBOSS)
dbigcgprogram(EMBOSS)
DDBJ(DNADataBankofJapan)
featuretable[SeeDDBJ/EMBL/GenBankfeaturekeytable]
flatfiles
example
fielddefinitions
locations[SeeDDBJ/EMBL/GenBanklocationexamplestable]
DDBJ/EMBL/GenBankfeaturetable
DDBJ/EMBL/GenBanklocationexamplestable
DDBJ/EMBL/GenBankqualifiertable
degapseqprogram(EMBOSS)
descriptionlines,FASTA

descseqprogram(EMBOSS)
dichetprogram(EMBOSS)
diffseqprogram(EMBOSS)
digestprogram(EMBOSS)
dinucleotideCG,scanningfor
dinucleotides,determiningnumberofinfiles
distmatprogram(EMBOSS)
DNAconstructs
linearmapsof,drawing
DNADataBankofJapan[SeeDDBJ]
DNAdoublehelixes,predictingbendingof
DNAsequencedatabases,searching
DNAsequences
displaying
predictingcutsitesin
predictingtwistingof
domainerprogram(EMBOSS)
domainscoordinatefiles,writingfromproteincoordinatefiles
dotmatcherprogram(EMBOSS)
dotpathprogram(EMBOSS)
dottupprogram(EMBOSS)
dregprogram(EMBOSS)

[TeamLiB]


BroughttoYouby


[TeamLiB]

[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
>(greaterthansign),FASTA
:(colon),EMBOSSUSAsyntax
|(verticalbar),Readseqformats

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
AAINDEXdatabase
aaindexextractprogram(EMBOSS)
ABIsequencetracefiles
abiviewprogram(EMBOSS)
alignmentformats,EMBOSS
alignwrapprogram(EMBOSS)
alternativeflatwormmitochondrialcode
alternativeyeastnuclearcode
aminoacids
chargesto
databaseofpropertiesof
propertiessummary
amino-acidmodifications
SWISS-PROTfeaturetable
frequentlyusedmodifications
lipidmoietyattachedgroups
antigenicprogram(EMBOSS)
antisense,outputting
applicationgroups,EMBOSS
ascidianmitochondrialcode

ASCIIfiles,removingcarriagereturnsfrom

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
backtranseqprogram(EMBOSS)
bacterialcode
bananaprogram(EMBOSS)
bases,searchingsequencesfor
BasicLocalAlignmentSearchTool[SeeBLAST]
BioJava
BioPerl
biosedutility(EMBOSS)
bl2seqprogram(BLAST)
BLAST(BasicLocalAlignmentSearchTool)
command-lineoptions
databases,indexing
programs
associatedsequencetypesand
server
supportforReadseq
BLAST-LikeAlignmentTool[SeeBLAT]
blastallprogram
blastpgpprogram(BLAST)
BLAT(BLAST-LikeAlignmentTool)
blepharismanuclearcode
btwistedprogram(EMBOSS)

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
caiprogram(EMBOSS)
carriagereturns,removingfromASCIIfiles
cDNAsequences,producingfromalignedproteinsequences
CGIwebserver,Readseqand
changeindicators,SWISS-PROTfeaturetable
chaosprogram(EMBOSS)
chargeprogram(EMBOSS)
checktransprogram(EMBOSS)
chipsprogram(EMBOSS)
chlorophyceanmitochondrialcode
ciliatecode
cirdnaprogram(EMBOSS)
ClustalW
command-lineoptions
emmaprogramasinterfaceto
codcmpprogram(EMBOSS)
code,genetic
alternativeflatwormmitochondrial
alternativeyeastnuclear
ascidianmitochondrial
bacterial
blepharismanuclear
chlorophyceanmitochondrial
ciliate
coelenteratemitochondrial

dasycladacean
echinoderm
euplotidnuclear
flatwormmitochondrial
hexamitanuclear
invertebratemitochondrial
mold
mycoplasma
plantplastid
protozoan
scenedesmusobliquusmitochondrial
spiroplasma
standard
thraustochytriummitochondrial
trematodemitochondrial
yeastmitochondrial
coderetprogram(EMBOSS)
codes
codingsequences,calculatingcodonfrequencytablefrom
nucleotide
CodonAdaptationIndex,calculating
codonfrequencytables
calculatingfromcodingfrequency
codonusagetablefiles
coelenteratemitochondrialcode
coiled-coilstructures,calculatingprobabilityof
colon(:),EMBOSSUSAsyntax
command-lineoptions
BLAST
BLAT

ClustalW
MEME
Readseq
comments,FASTA
compseqprogram(EMBOSS)
consprogram(EMBOSS)
consensussequence,calculatingfrommultiplesequencealignment
contactsprogram(EMBOSS)
coordinatefiles
reading


writingprotein-heterogencontactdatafilesfrom
CpGregions,identifying
CPGISLEdatabase,producingentryformatreports
cpgplotprogram(EMBOSS)
cpgreportprogram(EMBOSS)
crystalballprogram
Ctrl-Acharacters,NCBInonredundantdatabasesyntax
cuspprogram(EMBOSS)
cutsites,predictinginDNAsequences
CUTG,extractingdatafrom
cutgextractprogram(EMBOSS)
cutseqprogram(EMBOSS)

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]

EBI(EuropeanBioinformaticsInstitute)
echinodermcode
einvertedprogram(EMBOSS)
EMBL(EuropeanMolecularBiologyLaboratory)
CD-ROMformatindexfiles
buildingfromBLASTdatabase
buildingfromFASTAflatfiledatabase
buildingfromflatfiledatabase
featuretable[SeeDDBJ/EMBL/GenBankfeaturetable]
flatfiles
example
fielddefinitions
formatfiles
buildingfromindexingGCG-formatdatabase
convertingSCOPclassificationfilesto
writingSCOPclassiciationto
formatSCOPfiles,convertingtononredundantfiles
locations[SeeDDBJ/EMBL/GenBanklocationexamplestable]
qualifiertable[SeeDDBJ/EMBL/GenBankqualifiertable]
EMBOSS(EuropeanMolecularBiologyOpenSoftwareSuite)
alignmentformats
applicationgroups
datafiles,determiningdirectoriesthatcanhold
databases[SeeEMBOSSdatabases]
featureformats
helpdocumentationfor,displaying
programs
findingbykeywordsindocumentation
listingprogramsthatsharefunctionalitywith
tableof

reportformats
sequenceformats
input
output
UniformSequenceAddress(USA)
EMBOSSdatabases,searchingforsequenceswithspecifiedIDsornumbers
embossdatautility(EMBOSS)
embossversionprogram(EMBOSS)
emmaprogram(EMBOSS)
emowseprogram(EMBOSS)
entretprogram(EMBOSS)
enzymaticdatafiles,plotting
eprimer3program(EMBOSS)
equicktandemprogram(EMBOSS)
ESTsequences,trimmingpoly-Atailsoff
est2genomeprogram(EMBOSS)
etandemprogram(EMBOSS)
euplotidnuclearcode
EuropeanBioinformaticsInstitute[SeeEBI]
EuropeanMolecularBiologyLaboratory[SeeEMBL]
EuropeanMolecularBiologyOpenSoftwareSuite[SeeEMBOSS]
extractfeatutility(EMBOSS)
extractseqprogram(EMBOSS)

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
FASTA

flatfiledatabase,indexing
opensourcetoolsand
featureformats,EMBOSS
featuretables
DDBJ/EMBL/GenBank
extractingCDS/mRNA/translationsfrom
SWISS-PROT
writingrepresentationoftostandardoutput
features
locations
masking
qualifiers
tablesof[Seefeaturetables]
fielddefinitions
DDBJflatfiles
EMBLflatfiles
GenBankflatfiles
Pfamflatfiles
PROSITEflatfiles
SWISS-PROTflatfiles
files
ABIsequencetrace
ASCII,removingcarriagereturnsfrom
codonusagetable
coordinate
writingprotein-heterogencontactdatafilesfrom
dinucleotides,countingnumberof
domainscoordinatefiles,writingfromproteincoordinatefiles
EMBLCD-ROMformatindex
buildingfromBLASTdatabase

buildingfromFASTAflatfiledatabase
buildingfromflatfiledatabase
buildingfromGCG-formatdatabase
EMBL-likeformat,writingSCOPclassificationto
EMBOSSdata,determiningdirectoriesthatcanhold
enzymaticdataof,plottng
FASTA
sequenceentriesin
zzz[SeealsoFASTA][SeealsoFASTA]
flat[Seeflatfiles]
hexanucleotides,countingnumberof
inter-chainresidue-residuecontactdata
writing
intra-chainresidue-residuecontactdata
massspectrometryresult
PDB,parsing
profilematrix,creatingfromnucleicacidsequences
proteincoordinate
writingdomainscoordinatefilesfrom
writingfromPDBfiles
SCOPclassification
converting/writingtoEMBL-likeformatfiles
removinglow-resolutiondomainsfrom
removingredundantdomainsfrom
SWISS-PROT:PDB-equivalence,convertingtoEMBL-likeformat
trinucleotides,countingnumberof
typingsequencesinto
findkmprogram(EMBOSS)
flatfiledatabases,indexing
flatfiles

DDBJexample
EMBLexample
GenBankexample
Pfamexample


PROSITEexample
SWISS-PROTexample
flatwormmitochondrialcode
formatdbprogram
formatdbprogram(BLAST)
freakprogram(EMBOSS)
frequencytables,codon
funkyprogram(EMBOSS)
fuzznucprogram(EMBOSS)
fuzzproprogram(EMBOSS)
fuzztranprogram(EMBOSS)

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
G+Cpercentageofnucleicacidsequences,calculating2nd
gapsinalignedsequences,removing
GarnierOsguthorpeRobsonalgorithm(GORI)
garnierprogram(EMBOSS)
GCcontent,plottingoversequences
GCG-formatdatabases
geeceeprogram(EMBOSS)

GenBank
flatfiles
example
fielddefinitions
locations[SeeDDBJ/EMBL/GenBanklocationexamplestable]
geneticcode
alternativeflatwormmitochondrialcode
alternativeyeastnuclearcode
ascidianmitochondrialcode
bacterialcode
blepharismanuclearcode
chlorophyceanmitochondrialcode
ciliatecode
dasycladaceancode
echinodermcode
euplotidnuclearcode
flatwormmitochondrialcode
hexamitanuclearcode
invertebratemitochondrialcode
plantplastidcode
scenedesmusobliquusmitochondrialcode
standard
thraustochytriummitochondrialcode
trematodemitochondrialcode
yeastmitochondrialcode
getorfprogram(EMBOSS)
GORI(GarnierOsguthorpeRobsonalgorithm)
greaterthansign(>),FASTA
GRIBSKOVprofiles,findingmatcheswithsequences

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
helixturnhelixprogram(EMBOSS)
HENIKOFFprofiles,findingmatcheswithsequences
heterogengroups
convertingrawdictionarytoEMBL-likefileformat
parsedictionaryof
hexamitanuclearcode
hexanucleotides,determiningnumberofinfiles
hiddenMarkovmodel(HMM)
HMM(hiddenMarkovmodel)
generatingfordirectoryalignments
HMMERprograms
hmmgenprogram(EMBOSS)
hmomentprogram(EMBOSS)
hteparseprogram(EMBOSS)
hydrophobicmoment

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
iepprogram(EMBOSS)
infoalignutility(EMBOSS)
infosequtility(EMBOSS)
inter-chainresidue-residuecontactdatafiles,writing

interfaceprogram(EMBOSS)
InternationalNucleotideSequenceDatabaseCollaboration
intra-chainresidue-residuecontactdatafiles,writing
invertebratemitochondrialcode
invertedrepeatsinnucleotidesequences
isochoreprogram(EMBOSS)
isoelectricpoint

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
JavaAPIforEMBOSS
Jemboss

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
Kyte&Doolittlehydropathyplotofproteinsequences,displaying

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
lindnaprogram(EMBOSS)
listorprogram(EMBOSS)

locations
low-resolutiondomains,removingfromSCOPclassificationfiles

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
MAR/SARsites,findinginnucleicacidsequences
Markowmodels
marscanprogram(EMBOSS)
maskfeatprogram(EMBOSS)
maskseqprogram(EMBOSS)
massspectrometry
matchingdatainproteindatabases
MAST(MotifAlignmentandSearchTool)
command-lineoptions
examples
matcherprogram(EMBOSS)
megablastprogram(BLAST)
megamergerprogram(EMBOSS)
meltingtemperatureofnucleicacidsequences,calculating
MEME(MultipleEMforMotifElicitation)
command-lineoptions
examples
MEME/MAST
mergerprogram(EMBOSS)
modelorganisms
moldcode
molecularweights,findinginmassspectrometryresultfiles

msbarprogram(EMBOSS)
MultipleEMforMotifElicitation[SeeMEME]
multiplesequencealignment
calculating
consensussequencefrom
evolutionarydistancesbetween
EMBOSSformats
mwcontamprogram(EMBOSS)
mwfilterprogram(EMBOSS)
mycoplasmacode

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
NationalCenterforBiotechnologyInformation[SeeNCBI]
NationalInstitutesofHealth(NIH)
NationalLibraryofMedicine(NLM)
NCBI(NationalCenterforBiotechnologyInformation)
BLASTserver,syntaxfor
nonredundantdatabasesyntax
needleprogram(EMBOSS)
Needleman-Wunschglobalalignmentalgorithm
newcpgreportprogram(EMBOSS)
newcpgseekprogram(EMBOSS)
newseqprogram(EMBOSS)
NIH(NationalInstitutesofHealth)
NLM(NationalLibraryofMedicine)
noreturnprogram(EMBOSS)

notseqprogram(EMBOSS)
nrscopeprogram(EMBOSS)
nthseqprogram(EMBOSS)
nucleicacidsequences
calculatingG+Cof2nd
calculatingmeltingtemperatureof
creatingprofilematrixfilefrom
displayinginpublicationformat2nd
displayingproteintranslationinpublicationformat
findingMAR/SARsitesin
findingrecognitionsitesin
matchingtoregularexpressions
merging
scanningforsilentmutationrestrictionenzymesites
searchingwithPROSITE-styleproteinpatterns
translatingtopeptidesequences
nucleotidecodes
nucleotidesequences
invertedrepeatsin2nd
scanningfordinucleotideCG
scanningforrestrictionsites
searchingwithPROSITE-stylepatterns

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
octanolprogram(EMBOSS)
openreadingframes[SeeORFs]

opensourcetoolsforparsing/writingFASTAfiles
ORFs(openreadingframes)
outputtingsequencesof
plotting

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
pairwisesequencealignmentformats,EMBOSS
palindromeprogram(EMBOSS)
parsedictionaryofheterogengroups
pasteseqprogram(EMBOSS)
patmatdbprogram(EMBOSS)
patmatmotifsprogram(EMBOSS)
Pattern-HitInitiatedBLAST(PHI-BLASTÑseePHI-BLASTprogram)
patterns
PCRreactions,selectingprimersfor
PDBfiles,parsing
pdbparsprogram(EMBOSS)
pdbtospprogram(EMBOSS)
pepcoilprogram(EMBOSS)
pepinfoprogram(EMBOSS)
pepnetprogram(EMBOSS)
pepstatsprogram(EMBOSS)
peptidesequences
determiningwhereproteolyticenzymesmightcut
displayinginhelicalrepresentation
pepwheelprogram(EMBOSS)

pepwindowprogram(EMBOSS)
pepwindowallprogram(EMBOSS)
Pfam
flatfiles
example
fielddefinitions
PHI-BLAST(Pattern-HitInitiatedBLASTÑseePHI-BLASTprogram)
PHI-BLASTprogram(BLAST)
PROSITEconventions
phylogeneticanalysis
plantplastidcode
plotconprogram(EMBOSS)
plotorfprogram(EMBOSS)
polydotprogram(EMBOSS)
Position-SpecificIteratedBLAST(PSI-BLASTÑseePSI-BLASTprogram)
pregprogram(EMBOSS)
pressdbprogram
prettyplotprogram(EMBOSS)
prettyseqprogram(EMBOSS)
primerpairs,searchingagainstsequences
primer3program,eprimer3programasinterfaceto
primersearchprogram(EMBOSS)
PRINTSdatabases
preprocessingforusewithPSCANprogram
printsextractprogram(EMBOSS)
profgenprogram(EMBOSS)
profilematrixfiles,creatingfromnucleicacidsequences
profiles
profitprogram(EMBOSS)
programs

BLAST
EMBOSS
tableof
HMMER
prophecyprogram(EMBOSS)
prophetprogram(EMBOSS)
prosextractprogram(EMBOSS)
PROSITE
flatfiles
example
fielddefinitions
PHI-BLASTprogramand
PROSITEmotifdatabases
proteincoordinatefiles
writingdomainscoordinatefilesfrom


writingfromPDBfiles
proteindatabases,matchingmassspectrometrydatain
proteinfunctions,determining
proteinmotifs
comparingtoPROSITEmotifdatabase
comparingtoproteinsequences
findinghelix-turn-helixnucleicacidbindingin
identifyingquickly
proteinsequences
antigenicregions
calculatingmultiplealginmentof
chargestoaminoacids
creatingprofilematrixfilefrom

determiningnucleicacidsequencesource
displaying
publicationformat
displayinggraphofKyte&Doolittlehydropathyplotof
displayinginpublicationformat
metricsabout
producingcDNAsequencesfrom
reportsabout
searchingformatchofregularexpressionto
searchingwithPROSITE-stylepatterns
stopsin
proteinsignalcleavagesites,reporting
protein-heterogencontactdatafiles,writingfromcoordinatefiles
proteins
calculatingisoelectricpointof
displayingresiduesof
newlydiscovered
predictingtransmembranesegmentsin
proteincodingregions,analyzing
proteinhydropathy,displaying
scanningwithPRINTS
proteolyticenzymes
protozoancode
PSCANprogram
pscanprogram(EMBOSS)
PSI-BLAST(Position-SpecificIteratedBLASTÑseePSI-BLASTprogram)
PSI-BLASTprogram(BLAST)
psiblastprogram(EMBOSS)

[TeamLiB]

[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
qualifiers
DDBJ/EMBL/GenBankqualifiertable

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
Readseq
command-lineoptions
featuretableextractionoptions
formatssupported
REBASEdatabase
findingrecognitionsitesinnucleicacidsequences
searchingforspecifiedrestrictionenzymes
usingtopredictcutsitesinDNAsequences
rebaseextractprogram(EMBOSS)
recoderprogram(EMBOSS)
recognitionsites,findinginnucleicacidsequences
redataprogram(EMBOSS)
regions,SWISS-PROTfeaturetable
regularexpressions
matchingtonucleicacidsequences
matchingtoproteinsequences
remapprogram(EMBOSS)
reportformats,EMBOSS

residues,searchingsequencesfor
resourcesforfurtherinformation
aminoacids
BLAST
websites
BLAT
websites
ClustalW
websites
DDBJ
websites
EMBL
websites
EMBOSS
websites
GenBank
websites
geneticcode
HMM
HMMER
websites
Jemboss
MEME/MAST
NCBI
nucleicacids
Pfam
websites
PROSITE
websites
Readseq

SWISS-PROT
websites
restrictprogram(EMBOSS)
restrictionenzymes,searchingREBASEdatabasefor
reversesense,outputting
revseqprogram(EMBOSS)

[TeamLiB]


[TeamLiB]
[SYMBOL][A][B][C][D][E][F][G][H][I][J][K][L][M][N][O][P][Q][R][S][T][U][V][W][Y]
samplesequenceformats,FASTAentry
scenedesmusobliquusmitochondrialcode
SCOPclassificationfiles
scopalignprogram(EMBOSS)
scopeprogram(EMBOSS)
scopnrprogram(EMBOSS)
scopparseprogram(EMBOSS)
scoprepprogram(EMBOSS)
scopresoprogram(EMBOSS)
scopseqsprogram(EMBOSS)
secondarystructures
predicting2nd
SWISS-PROTfeaturetable
seealsoprogram(EMBOSS)
seedalignments
seqalignprogram(EMBOSS)
seqmatchallprogram(EMBOSS)
seqretprogram(EMBOSS)

seqretsplitprogram(EMBOSS)
seqsearchprogram(EMBOSS)
seqsortprogram(EMBOSS)
sequenceanalysis
subfieldsof
toolsforperforming,listof
sequenceannotation
sequencedatalines,FASTA
sequencedatabases
MASTand
tablelistingwaystoaccess
sequenceformats
EMBOSS
input
output
FASTA[SeeFASTA]
sequences
aligned
alignmentformats
plottingqualityofconservationof
removinggapsfrom
usingSmith-Watermanalgorithm
cDNA,producingfromalignedproteinsequences
comparing2nd
all-against-allpairwise
matchingwordsofspecifiedlength
nonoverlappingwordmatchplotdisplay
comparing/matchingwithBLAST
concatenating
CpGareasin

creatinggamerepresentationplotsfor
descriptivetextof,searching
displaying
DNA
predictingcutsitesin
predictingtwistingof
editing2nd
EST,trimmingpoly-Atailsoff
excluding
extracting
pairsof
findingmatcheswithGRIBSKOV/HENIKOFFprofiles
findingoptimumalignmentof
identifyingCpGregionsin
insertingoneintoanother
listinginformationabout2nd
listingpropertiesof


maskingfeaturesof
matching
merging
multiplealignment
calculatingconsensussequencefrom
calculatingevolutionarydistancesbetween
mutating
namesof,addingtolistfile
nucleicacid
calculatingfractionofG+Cbasesof
calculatingmeltingtemperatureof

calculatingmultiplealignmentof
calculatingpercentG+Cof
creatingprofilematrixfilefrom
displayinginpublicationformat2nd
displayingproteintranslationinpublicationformat
findingMAR/SARsitesin
findingrecognitionsitesin
matchingtoregularexpressions
merging
scanningforsilentmutationrestrictionenzymesites
searchingwithPROSITE-styleproteinpatterns
translatingtopeptidesequences
nucleotide
invertedrepeatsin2nd
scanningfordinucleotideCG
scanningforrestrictionsites
searchingwithPROSITE-stylepatterns
ofORFs
outputtingreversecomplementof
peptide
determiningwhereproteolyticenzymesmightcut
displayinginhelicalrepresentation
translatingtonucleicacidsequences
plottingGCcontentover
protein[Seealsoproteinsequences][Seealsoproteinsequences]
searchingformatchofregularexpressionto
randomlyshufflingorderof
reading/writing
inindividualfiles
regionsof

maskingoff
removing
reportingdifferencesbetween
retrievingfromSWISS-PROT
scanningfortandemrepeats
searchingEMBOSSdatabasesfor
searchingforbases/residues
searchingprimerpairsagainst
setof,comparing
skipping
splicednucleotide,aligningtounsplicedgenomicDNAsequences
strippingvectorsequencesfrom
tandemrepeatsin
tidyingupendsof
TRANSFAC,matchingagainstinputsequences
typingintofiles
seqwordsprogram(EMBOSS)
setdbprogram
showalignprogram(EMBOSS)
showdbprogram(EMBOSS)
showfeatprogram(EMBOSS)
showorfprogram(EMBOSS)
showseqprogram(EMBOSS)
shuffleseqprogram(EMBOSS)
SIB(SwissInstituteofBioinformatics)
sidechainsofaminoacids
sigcleaveprogram(EMBOSS)
siggenprogram(EMBOSS)