TOC for bioperl-live::Bio::Tools
AlignFactoryBase object for alignment factories
AmpliconSearchFind amplicons in a template using degenerate PCR primers
AnalysisResultBase class for analysis result objects and parsers
Blatparser for Blat program
CodonTableCodon table object
Coilparser for Coil output
ECnumberrepresentation of EC numbers (Enzyme Classification)
EPCRParse ePCR output and make features
ERPINa parser for ERPIN output
ESTScanResults of one ESTScan run
EponineResults of one Eponine run
Est2GenomeParse est2genome output, makes simple Bio::SeqFeature::Generic objects
Fgeneshparse results of one Fgenesh run
FootPrinterwrite sequence features in FootPrinter format
GFFA Bio::SeqAnalysisParserI compliant GFF format parser
GelCalculates relative electrophoretic migration distances
GeneidResults of one geneid run
GenemarkResults of one Genemark run
GenewiseResults of one Genewise run
GenomewiseResults of one Genomewise run
GenscanResults of one Genscan run
Glimmerparser for Glimmer 2.X/3.X prokaryotic and GlimmerM/GlimmerHMM eukaryotic gene predictions
GrailResults of one Grail run
GuessSeqFormatModule for determining the sequence format of the contents of a file, a string, or through a filehandle.
HmmpfamParser for Hmmpfam program
IUPACGenerates unique sequence objects or regular expressions from an ambiguous IUPAC sequence
InfernalA parser for Infernal output
LucyObject for analyzing the output from Lucy, a vector and quality trimming program from TIGR
MZEFResults of one MZEF run
MatchParses output from Transfac's match(TM)
OddCodesObject holding alternative alphabet coding for one protein sequence
Primer3Create input for and work with the output from the program primer3
PrintsParser for FingerPRINTScanII program
Profileparse Profile output
Promoterwiseparser for Promoterwise tab format output
PrositeScanParser for ps_scan result
Protparamsubmit to and parse output from protparam ;
PseudowiseResults of one Pseudowise run
QRNAA Parser for qrna output
RNAMotifA parser for RNAMotif output
RandomDistFunctionsA set of routines useful for generating random data in different distributions
RepeatMaskera parser for RepeatMasker output
Segparse C output
SeqPatternrepresent a sequence pattern or motif
SeqStatsObject holding statistics for one particular sequence
SeqWordsObject holding n-mer statistics for a sequence
SiRNAPerl object for designing small inhibitory RNAs.
SigcleaveBioperl object for sigcleave analysis
Signalpparser for Signalp output
TandemRepeatsFindera parser for Tandem Repeats Finder output
TargetPResults of one TargetP run
Tmhmmparse TMHMM output (TransMembrane HMM)
dpAlignPerl extension to do pairwise dynamic programming sequence alignment
ipcressParse ipcress output and make features
isPcrParse isPcr output and make features
pICalculatorcalculate the isoelectric point of a protein
pSWpairwise Smith Waterman object
tRNAscanSEA parser for tRNAscan-SE output