Bionformatics for Comparative (Organelle) Genomics

The bioinformatics tools listed below assist in genome sequence analysis and megasequencing project management. They have been developed mostly in the context of the Organelle Genome Megasequencing Program (OGMP).

See also tools developed in the context of the Protist EST Project (PEP).

All tools available upon request

The following tools use generally the FASTA format. Many of them also read from or write to an OGMP MASTERFILE (MF), a text-based file for maintaining a DNA sequence together with its embedded feature annotations and notes.

• Tools for batchwise sequence similarity search and output browsing:
  • BBLAST, batch BLAST searcher
  • BOB, text based BBLAST output browser
  • BFASTA, local batch fasta searcher
  • FOB, text based BFASTA output browser
• Tools for sequence submission and publication:
  • MF2SQN, for automated submission of annotated DNA sequences in MF format
  • MF2MAP, for production of a gene coordinate file from an annotated sequence file in MF format, to aid in the construction of genetic maps
  • MAPIT, for automatic generation of postscript files representing circular genetic maps that optimizes spacing of the graphical elements
• Decision support tools:
  • SPAM, decision tool for managing an ongoing sequencing project
  • MFMAIN, automatically inserts annotations into a DNA sequence file
  • WATSTATS, predicts genome size, number of contigs or number of required readings using formulas from M. Waterman
• Tools assisting DNA sequence analysis:
  • FLIP, basic sequence analysis tool (ORF identification, conversion to reverse/complementary strand)
  • PEPPER, extracts proteins from an annotated DNA sequence file, based on feature annotations
  • FINDREP, simple brute-force searcher for perfect repeats in sequences
  • PROTFILT, filters ORFs deduced from a DNA sequence on the basis of size, start codon or overlap with genes.
  • NO_BLAST and NO_FASTA are scripts that peform remote BLAST searches and local FASTA searches only on those ORFs in a masterfile that have not yet been annotated.
• Tools designed for the OGMP annotation maintenance system:
  • CLEANMF, a validator and checker of annotation syntax and logic for a sequence file in MF format
  • COSMEA has essentially the functionality of mf2stad and stad2mf together, but employs a different approach. While the two latter programs insert annotations into a new masterfile version by using sequence tags and the Staden assembler, COSMEA calculates the position of annotations in relation to the start point of readings. This procedure is more robust when long repeats are present.
  • READ2PHRAP integrates all tools and automatically executes and validates all steps involved in the processing of newly generated sequence data. Trace files (readings from the automatic sequencer) serve as input and the process terminates with the completed assembly.
• File format conversion. Numerous tools have been written to interface with phylogeny programs, FASTA, the GDE environment, etc.

[ OGMP | GOBASE | FMGP | PID ]

Last update: 13 June 2011, GB.