1. n
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Kazuharu Arakawa
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Institute for Advanced Biosciences, Keio University
Graduate School of Media and Governance
Expertise: Bioinformatics, Systems Biology
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2. G-language
Web Service Interface
Institute for Advanced
Biosciences, Keio University
KAZUHARU ARAKAWA
NOBUHIRO KIDO
KAZUKI OSHITA
MASARU TOMITA
2009.06.27

3. G-language Project
• First release in 2001 (Now 1.8.8)
• Perl library, interactive shell, 100+ applications, GUI
• Focus on analysis of bacterial genomes.
• compatible with BioPerl (10~50x faster for manipulating
genome flatfile) Arakawa et al. (2003) Bioinformatics
Arakawa et al. (2006) Journal of Pesticide Science
• http://www.g-language.org/ Arakawa et al. (2008) Genes Genomes Genomics
Arakawa et al. (2009) BMC Bioinformatics

5. BAS_engine _eri_reader blastcutting graphical_LTR_search redundancy_fasta
BAS_parser _eri_update_with_kegg blastparser icdi redundancy_sim4
BAS_scripter _fasta bui leading_strand rep_ori_ter
CHI_engine _file_list_for_mapping cai load_kegg_api rmpolya
CHI_parser _find_bad_substance calc_pI load_kegg_api3 rscu
CHI_scripter _find_pathway_gap cap3_parse load_rcluster run_glimmerM
COMGA_correlation _foreach_blastpointer_for_mapping cbi longest_ORF sdb_load
COMGA_engine _foreach_mask_repeat_for_mapping cds_echo ma_filter sdb_save
COMGA_parser _formatdb cei ma_normalize seq2png
COMGA_scripter _formatdb_for_mapping cluster ma_rfilter seqinfo
COMGA_table_maker _gblaster codon_compiler mapping_blast2 set_cogpath
DONT_USE_ERRO _h2v codon_counter mapping_sim4 set_goa
GEMS_engine _hmmpfam codon_usage markov set_gpac
GEMS_parser _jstat_for_STeP
100+
cognitor maskseq set_operon
GEMS_scripter _jstat_for_mapping complement match_test shannon_cu
KeySearch _key_printer consensus_z molecular_weight sim4_parse
PubMedSearch _list_clusterer cum_gcskew msg_ask_interface splitprintseq
RNAfold _list_sorter diffseq msg_error ss2er
STeP_engine _makegaplist dignitor msg_gimv stderr
STeP_parser _mask_repeat_for_mapping ecell msg_interface stdin
STeP_scripter _oligomer_translation eliminate_atg msg_percent stdout
_R_RNA_graph _over_lapping_printer eliminate_pat msg_progress substance_layout
_R_base_graph _post_blast_clusterer enc msg_send substance_layout2
_STS_divider_for_STeP _print_tandem enzyme_layout msg_set_gimv test_gpac
_STS_modifer_for_STeP _repeatmasker equitability msg_system_console translate
_UniMultiGrapher _sdb_path er2eri msg_term_console usage_dist
_UniUniGrapher _set_sdb_path fasta_parse oligomer_counter valid_CDS
_acc2ftp_bacteria _sim4 file_maker opt_as_gb view_cds
_base_printer _sts2pg_for_STeP file_maker_fasta opt_default w_value
_blast _translate find_dnaAbox opt_get
_blast_db_for_mapping _trf find_identical_gene opt_val
_blast_for_mapping _value_printer find_king_of_gene ori_search
_blast_tp_finder aa_codon_compiler find_ori_ter output_maker
_blastpointer_for_mapping aa_codon_usage find_seq over_lapping_finder
_cap3 aaui find_tandem palindrome
_clustalw alignment fop pasteseq
_codon_amino_printer amino_counter foreach_RNAfold peptide_mass
_codon_table amino_info foreach_tandem phx
_codon_usage_printer annotate_with_glimmerM form_sim4 plasmid_map
_codon_usage_table atcgcon funcD print_gene_function_list
_complement base_counter gcskew pseudo_atg
_csv_h2v base_entropy gcwin qstat
_cutquery_for_mapping base_individual_information_matrix genome_map qsub
_distance_cu base_information_content genome_map2 query_strand
_ePCR_for_STeP base_relative_entropy genomicskew read_goa
_ecell_name2kegg_compound base_z_value gopac redundancy
_eri_extracter blast_parse gpac redundancy_cap3

6. Perl API: BioPerl vs G
use Bio::SeqIO;
$in = Bio::SeqIO->new(-file=>"ecoli.gbk", '-format'=>'GenBank');
$seq = $in->next_seq();
foreach $feat ($seq->all_SeqFeatures()){
next unless($feat->primary_tag eq ‘CDS’);
print $feat->each_tag_value(“note”), “¥n”;
}
use Bio::DB::GenBank;
use Bio::Seq;
$gb = new Bio::DB::GenBank;
$seq = $gb->get_Seq_by_acc(“NC_000913”);
use G;
$gb = load ecoli; # $gb = load(“genbank:NC_000913”);
foreach $cds ($gb->cds()){
say $gb->{$cds}->{note};
}

7. Interactive Shell
• fully functional Perl shell
• basic UNIX commands
• mix of the above (weird)
• print togoWS(‘NC_000908’) |head -n 10 |wc > out.txt
• tab completion (file, functions), history, editing with
EMACS key binding
• persistent data
• logging
• search for functions (like wossname in EMBOSS) and
reading documentations (like tfm in EMBOSS), both for
G-language API and BioPerl classes
• database search (NCBI, KEGG, UniProt ... and more)
• sequence and data retrieval

8. Web Service Interface - Overview
Deveopment supported by BioHackathon 2009 in Okinawa, Japan

9. REST Interface http://rest.g-language.org
http://useG.jp
1. Accessing genome flatfile data
http://useG.jp/[species]/[gene]/[feature]
a. http://useG.jp/ecoli/ - Nucleotide composition of E.coli genome
b. http://useG.jp/ecoli/recA - Feature information about recA gene
c. http://useG.jp/ecoli/recA/start - Start position of recA gene
d. http://useG.jp/ecoli/*/translation - Amino acid sequence of all genes (FASTA)
2. Manipulating genome data
http://useG.jp/[species]/[gene]/[method]/[option=value]/...
a. http://useG.jp/method_list/gb - List all available methods
b. http://useG.jp/NC_000913/*/before_startcodon - Retrieve upstream sequence of all genes
3. Genome sequence analysis
http://useG.jp/[species]/[method]/[option=value]/...
a. http://useG.jp/method_list/ - List all available methods
b. http://useG.jp/mgen/gcskew/window=1000/ - GC skew of M.genitalium with
c. http://useG.jp/mgen/gcskew/cumulative=1/output=f/ 1000bpwindows
- Get the raw GC skew result as
CSV data
4. Other methods (not requiring genome sequence input)
http://useG.jp/[method]/[option=value]/...
a. http://useG.jp/togoWS/C00001 - Retrieve KEGG C00001 through togoWS
b. http://useG.jp/help/gcskew - Show manual for gcskew method

10. AJAX/CGI Interface http://ws.g-language.org/atelier/

11. Bio::Glite - light weight version using the REST service
32kb in size,
only requires LWP::UserAgent
easy install via “cpan Bio::Glite”

12. SOAP Service
http://soap.g-language.org/g-language.wsdl

13. Works with
Taverna2
9 example workflows
are already available
at

15. ISMB Posters
Poster U16
Command-line-based integration of online bioinformatics resources
Kazuki Oshita, Kazuharu Arakawa, Masaru Tomita
Poster U22
G-language Genome Analysis Environment Version 2: Integrated
workbench for computational genome sequence analysis
Kazuharu Arakawa, Masaru Tomita
Poster X023
Automatic layout tool for large-scale metabolic pathway models based
on KEGG Atlas and SBML/SBGN
Nobuhiro Kido, Nobuaki Kono, Kazuharu Arakawa, Masaru Tomita
Poster X031
Pathway Projector: Web-based Zoomable Pathway Browser using
KEGG Atlas and Google Maps API
Nobuaki Kono, Kazuharu Arakawa, Nobuhiro Kido, Ryu Ogawa, Kazuki
Oshita, Keita Ikegami, Satoshi Tamaki, Masaru Tomita

16. Nobuhiro the REST/CGI server
deveoloped
Kido Kazuki Oshitaserver
deveoloped the SOAP
Acknowledgements
BioHackathon 2009 sponsored by DBCLS and OIST of Japan
Yamagata Prefectural Government and Tsuruoka City.