Software Tools :: Gene Finding and Codon Analysis
Background
Gene Finding and Codon Analysis
References
Programs
Combination methods
- GLIMMER 2 system: finding genes in microbial genome sequences [local access only]
Search by content
- GCG Programs
- TestCode: Plots Fickett's TESTCODE statistic
- Frames: Plots open reading frames
- CodonPreference: Plots Gribskov's codon preference statistic
- EMBOSS Programs
- getorf: Finds and extracts open reading frames (ORFs)
- showorf: Displays pretty output of DNA translations
- plotorf: Plots potential open reading frames
- showseq: Displays a sequence with features, translation, etc.
- syco: Plots synonymous codon usage (Gribskov statistic)
Search by signal
- GCG Programs
- Terminator: Searches for prokaryotic factor-independent RNA polymerase terminators
- Map: Searches for transcription factors using tfsites.dat file
- MapPlot: Plots locations of transcription factors using tfsites.dat file
- FindPatterns: Searches for short user-specified patterns
- EMBOSS Programs
- cpgplot: Plots CpG-rich areas
- cpgreport: Reports all CpG-rich regions
- newcpgseek: Reports CpG-rich regions
- newcpgreport: Reports CpG-rich areas in CPGISLE database entry format
- marscan: Finds MAR/SAR sites in nucleic sequences
- fuzznuc: Searches for nucleic acid patterns
- dreg: Searches for regular expressions in a nucleotide sequence
Search by homology
- EMBOSS Programs
- est2genome: Aligns an EST sequence to a genomic DNA sequence
Related Tools
- GCG Programs
- Correspond: Compares codon usage tables
- CodonFrequency: Creates a codon usage table
- EMBOSS Programs
- cusp: Creates a codon usage table
- chips: Computes codon usage statistics
- codcmp: Compares codon usage tables
- coderet: Extracts CDS, mRNA and translations from feature tables
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