| AlignFactory | Base object for alignment factories |
| AnalysisResult | Base class for analysis result objects and parsers |
| BPbl2seq | Lightweight BLAST parser for pair-wise sequence
alignment using the BLAST algorithm. |
| BPlite | Lightweight BLAST parser |
| BPpsilite | Lightweight BLAST parser for (iterated) psiblast reports |
| Blat | parser for Blat program |
| CodonTable | Bioperl codon table object |
| Coil | parser for Coil output |
| ECnumber | representation of EC numbers (Enzyme Classification) |
| EPCR | Parse ePCR output and make features |
| ERPIN | a parser for ERPIN output |
| ESTScan | Results of one ESTScan run |
| Eponine | Results of one Eponine run |
| Est2Genome | Parse est2genome output, makes simple Bio::SeqFeature::Generic objects |
| Fgenesh | parse results of one Fgenesh run |
| FootPrinter | write sequence features in FootPrinter format |
| GFF | A Bio::SeqAnalysisParserI compliant GFF format parser |
| Gel | Calculates relative electrophoretic migration distances |
| Geneid | Results of one geneid run |
| Genemark | Results of one Genemark run |
| Genewise | Results of one Genewise run |
| Genomewise | Results of one Genomewise run |
| Genscan | Results of one Genscan run |
| Glimmer | parser for GlimmerM/GlimmerHMM eukaryotic gene predictions |
| Grail | Results of one Grail run |
| GuessSeqFormat | Module for determining the sequence
format of the contents of a file, a string, or through a
filehandle. |
| HMM | Perl extension to perform Hidden Markov Model calculations |
| Hmmpfam | Parser for Hmmpfam program |
| IUPAC | Generates unique Seq objects from an ambiguous Seq object |
| Lucy | Object for analyzing the output from Lucy,
a vector and quality trimming program from TIGR |
| MZEF | Results of one MZEF run |
| OddCodes | Object holding alternative alphabet coding for
one protein sequence |
| Primer3 | Create input for and work with the output from
the program primer3 |
| Prints | Parser for FingerPRINTScanII program |
| Profile | parse Profile output |
| Promoterwise | parser for Promoterwise tab format output |
| PrositeScan | Parser for ps_scan result |
| Pseudowise | Results of one Pseudowise run |
| QRNA | A Parser for qrna output |
| RNAMotif | A parser for RNAMotif output |
| RandomDistFunctions | A set of routines useful for
generating random data in different distributions |
| RepeatMasker | a parser for RepeatMasker output |
| RestrictionEnzyme | Bioperl object for a restriction endonuclease
(cuts DNA at specific locations)
DEPRECATED. Please use the Bio::Restriction modules instead. |
| Seg | parse C output |
| SeqPattern | represent a sequence pattern or motif |
| SeqStats | Object holding statistics for one
particular sequence |
| SeqWords | Object holding n-mer statistics for a sequence |
| SiRNA | Perl object for designing small inhibitory RNAs. |
| Sigcleave | Bioperl object for sigcleave analysis |
| Signalp | parser for Signalp output |
| Tmhmm | parse TMHMM output (TransMembrane HMM) |
| dpAlign | Perl extension to do pairwise dynamic programming sequence alignment |
| ipcress | Parse ipcress output and make features |
| isPcr | Parse isPcr output and make features |
| pICalculator | calculate the isoelectric point of a protein |
| pSW | pairwise Smith Waterman object |
| tRNAscanSE | A parser for tRNAscan-SE output |