Software Tools :: Motifs, Patterns, and Profiles
Background
Motifs, Patterns and Profiles
Programs
Searching sequences for simple user-specified patterns
- GCG Programs
- FindPatterns: Searches sequence(s) for short patterns
- EMBOSS Programs
- dreg: Regular expression search of a nucleotide sequence
- preg: Regular expression search of a protein sequence
- fuzznuc: Nucleic acid pattern search (PROSITE format)
- fuzzpro: Protein pattern search (PROSITE format)
- fuzztran: Protein pattern search after translation (PROSITE format)
- patmatdb: Searches a set of proteins with a motif in PROSITE format
Searching databases of known patterns and motifs with a sequence
- GCG Programs
- Motifs: Searches the PROSITE Dictionary of Protein Sites and Patterns with a protein sequence
- Map: Locates transcription factors using tfsites.dat file
- MapPlot: Plots locations of transcription factors using tfsites.dat file
- EMBOSS Programs
- patmatmotifs: Searches a PROSITE motif database with a protein sequence
- pscan: Searches the PRINTS database of protein motif fingerprints with a protein
- tfscan: Scans DNA sequences for transcription factors
Finding potential functional patterns and motifs
- GCG Programs
- Terminator: Finds prokaryotic factor-independent RNA polymerase terminators
- HTHScan: Finds helix-turn-helix motifs in protein sequences
- SPScan: Finds possible signal sequence cleavage sites in protein sequences
- EMBOSS Programs
- isochore: Plots isochores in large DNA sequences
- cpgplot: Plots CpG-rich areas
- cpgreport: Reports all CpG-rich regions
- newcpgreport: Reports all CpG-rich areas
- newcpgseek: Reports CpG-rich regions
- marscan: Finds MAR/SAR sites in nucleic sequences
- helixturnhelix: Reports nucleic acid binding motifs in a protein sequence
- sigcleave: Reports protein signal cleavage sites
Creating and using profiles
- GCG Programs
- ProfileMake: Creates a Gribskov profile from a set of aligned sequences
- ProfileGap: Aligns a profile to one or more sequences
- ProfileScan: Searches a database of protein profiles with a protein sequence
- ProfileSearch: Searches a set of sequences or a sequence database with a profile
- ProfileSegments: Creates optimal profile-sequence alignments from ProfileSearch results
- EMBOSS Programs
- prophecy: Creates a frequency matrix or a profile from a multiple sequence alignment
- prophet: Aligns a profile created by prophecy to one or more sequences
- profit: Scans one or more sequences with a frequency matrix created by prophecy
Creating and using hidden Markov model (HMM) profiles
- GCG Programs
- HmmerBuild: Creates a profile HMM from aligned sequences
- HmmerCalibrate: Calibrates existing profile HMMs for more sensitive searches
- HmmerPfam: Searches a database of profile HMMs (such as Pfam) with a sequence
- HmmerSearch: Searches a sequence database with a profile HMM
- HmmerAlign: Aligns one or more sequences to a profile HMM
- HmmerEmit: Randomly generates sequences that match a given profile HMM
- HmmerConvert: Converts between HMM and Gribskov profile formats
- HmmerIndex: Indexes a database of profile HMMs for use by HmmerFetch
- HmmerFetch: Retrieves a profile HMM by name from an indexed profile HMM database
Discovering new motifs in your sequences
- GCG Programs
- MEME: Examines a set of unaligned sequences to find shared motifs
- MotifSearch: Searches a set of sequences with a motif found by MEME
Related Tools
- GCG Programs
- Window: Creates a frequency table of short sequence patterns within a sliding window
- StatPlot: Plots the frequency table data created by Window
- EMBOSS Programs
- freak: Residue/base frequency table or plot
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