Architecture

The Development and Design of a Generic Genome Analysis Environment: The G-language system

English

Japanese

Manual

	Prelude-manual	English	Japanese
	perldoc SubOpt	English	Japanese
	perldoc Rcmd	English	Japanese
	G-language Manager	English	Japanese

Tutorial

	GCskew	English	Japanese	Calculates GC skew
	Codon usage	English	Japanese	Refers to the number of codons and amino acids per CDS, and caluculates the codon usage
	BAS	English	Japanese	Bacteria analysis system

Documentation of All Modules

Modules of G-language Genome Analysis Environment 1.6.9 Modules of G-language Genome Analysis Environment 1.6.7 Modules of G-language Genome Analysis Environment 1.6.4

Subroutines

MT::SEQ class

	MT::SEQ::Align class
	diffseq
	alignment
	MT::SEQ::Tandem class
	find_tandem	Finds and extracts tandem repeats from DNA sequences
	foreach_tandem	Finds each length and pattern of repeats from a sequence
	_print_tandem	Prints results of find_tandem
	MT::SEQ::OverLapping class
	overlapping_finder
	_over_lapping_printer	Prints the result of over_lapping_finder
	MT::SEQ::FreeEnergy class
	Rnafold	Calculates the nucleotide's free energy, and estimates the secondary structure, using RNA fold
	foreach_RNAfold	Divides the specified region into windows, and calculates the free energy of each
	MT::SEQ::Consensus class
	base_counter	Counts bases to find consensus sequences around the start/end codon
	_base_printer	Prints the result of base_counter
	_base_entropy	Calculates the entropy of base_counter
	_base_information_content	Information content of base_counter
	_base_relative_entropy	Calculates the relative entropy of base_counter
	_base_z_value	Calculates the Z-value of the base_counter
	_base_individual_information_matrix
	consensus_z
	MT::SEQ::Codon class
	codon_counter	Counts the number of codons in CDS
	amino_counter	Counts the number of aminos in CDS
	codon_usage	Calculates the codon usage in one CDS
	_codon_amino_printer	Prints the results of codon or amino counter
	_codon_usage_printer	Prints the result of codon usage
	MT::SEQ::eliminate class
	eliminate_atg	Eliminates sequences with "atg" in the same frame
	eliminate_pat	Eliminates sequences which have patterns in a specified range
	valid_cds	Choose valid CDS
	MT::SEQ::PatSearch class
	Oligomer_counter	Counts oligomers within specified window
	find_seq	Counts an oligomer and its complement
	palindrome	Searches for palindrome sequences
	MT::SEQ::GCskew class
	find_ori_ter	Predicts the replicational origin and terminus
	gcskew	Calculates the GC skew
	cum_gcskew
	genomic_skew
	gcwin	Calculates the cumulative GC skew
	view_cds	Creates a graph showing the average A, T, G, C contents around the start/stop codons
	MT::SEQ::Util class
	atcgcon	Calculates the atgc content of all CDS withing the genome
	cds_echo	Displays the starting and ending positions of a CDS
	print_gene_function_list	Prints the number of genes for each function, and the number of specified oligomers in each gene function group. The default for string sequence is 'gctggtgg'
	seq2gif	Converts a sequence to a gif image
	genome_map	Calculates CAI values for each genes, and inputs in the G instance
	mask_seq	The portion specified under sequence is replaced by N
	past_seq
	MT::SEQ::CAI class	Insert sequence in the part specified under sequence
	cai	Calculates CAI values for each genes, and inputs in the G instance
	w_value	Calculates the W value necessary for CAI analysis
	MT::SEQ::ORF class
	longest_ORF	Searches for the longest ORF
	pseudo	Gets the upstream and downstream sequence from "pseudo ATG", ATG codon that is not a start codon
	find_identical_gene	Finds identical genes in 2 genomes. The returned array is an array of CDS numbers of genome 1
	MT::SEQ::Markov class
	markov	Calculates the Markov analysis for all oligomers of specified length

MT::Tools class

	MT::Tools::Graph class
	_UniUniGrapher	Creates a two dimensional graph with gnuplot
	_UniMultiGrapher	Creates a two dimensional graph with gnuplot
	MT::Tools::H2v class	Prepares the query file by dividing the long Fasta file to short files per every gene
	_csv_h2v	Reverses the rows and columns of an array of array
	_h2v
	MT::Tools::Mapping class
	_mask_repeat_for_mapping	Applies RepeatMasker on sequences
	_foreach_mask_repeat_for_mapping	Runs mask_repeat for each query file in the specified directory
	_cutquery_for_mapping	Prepares the query file by dividing the long Fasta file to short files per every gene
	_blastpointer_for_mapping	Reads in the results of BLAST, and extracts the mapped data with e-values lower than E-150
	_file_list_for_mapping	creates a list of the query files
	_blast_for_mapping	Applies blast by the specification of the database and query directory
	_blast_db_for_mapping	Prepares the subject for BLAST by inserting enters at every assigned number of nucleotide bases
	_formatdb_for_mapping	Runs formatdb on all subject files to create a database
	_foreach_blastpointer_for_mapping	Runs blastpointer for each output file of BLAST
	MT::Tools::Blast class
	_blast_tp_finder	Extracts the e-value, starting and ending positions of the query and database, and the strand from the BLAST result file
	blaster

MT:Ecell class

	MT::Ecell::Pathway class
	find_bad_badsubstance	Finds bad substances from e-cell rule files
	find_pathway_gap	Locates pathway gaps in e-cell rule files
	MT::Ecell::Reader class
	eri_reader	Reads in e-cell rule files
	eri_extracter	Prints E-cell eri(rule) files
	MT::Ecell::KEGG class
	eri_update_with_kegg	Matches the ecell name with KEGG compound and prints the chemical formula
	ecell_name2kegg_compound	Matches the ecell name with KEGG compound by original scoring system