Architecture

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


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