[Bioperl-l] Is Bio::KEGG:Enzyme implemented?

[Brian Osborne]

Hey Bryan,

Bio::SeqIO::kegg parses the database format and creates Seq objects, I  
show an example of the format below.

Brian O.


ENTRY       10768             CDS       H.sapiens
NAME        AHCYL1
DEFINITION  S-adenosylhomocysteine hydrolase-like 1 [EC:3.3.1.1]
ORTHOLOG    KO: K01251  adenosylhomocysteinase
CLASS       Metabolism; Amino Acid Metabolism; Methionine metabolism
             [PATH:hsa00271]
             Metabolism; Metabolism of Other Amino Acids; Selenoamino  
acid
             metabolism [PATH:hsa00450]
POSITION     
1:join(26813..26932,50794..50905,52974..53117,54122..54222,54657..
              
54759,56523..56617,57185..57291,58104..58220,58427..58490,59255..
              
59343,59706..59776,60133..60227,60312..60410,60811..60879,61308..
             61386,62491..62611,63434..63440)
DBLINKS     LocusLink: 10768
             GDB: 9958257
             NCBI: 21361647
             SP: O43865
CODON_USAGE       T               C               A               G
           T   7   8   1  10   8  10   6   2   7  11   1   0  11   8    
0   8
           C   3  10   2  16   3   8   4   3   2   6   6  17   3   6    
7   3
           A   9  15   3  14   6  11  15   1  11  11  14  24   2   8    
2   4
           G  10   9   7  17  18  11  11   3  21  11  10  23   5  11    
6  11
AASEQ       530
              
MSMPDAMPLPGVGEELKQAKEIEDAEKYSFMATVTKAPKKQIQFADDMQEFTKFPTKTGR
              
RSLSRSISQSSTDSYSSAASYTDSSDDEVSPREKQQTNSKGSSNFCVKNIKQAEFGRREI
              
EIAEQDMSALISLRKRAQGEKPLAGAKIVGCTHITAQTAVLIETLCALGAQCRWSACNIY
              
STQNEVAAALAEAGVAVFAWKGESEDDFWWCIDRCVNMDGWQANMILDDGGDLTHWVYKK
              
YPNVFKKIRGIVEESVTGVHRLYQLSKAGKLCVPAMNVNDSVTKQKFDNLYCCRESILDG
              
LKRTTDVMFGGKQVVVCGYGEVGKGCCAALKALGAIVYITEIDPICALQACMDGFRVVKL
              
NEVIRQVDVVITCTGNKNVVTREHLDRMKNSCIVCNMGHSNTEIDVTSLRTPELTWERVR
              
SQVDHVIWPDGKRVVLLAEGRLLNLSCSTVPTFVLSITATTQALALIELYNAPEGRYKQD
             VYLLPKKMDEYVASLHLPSFDAHLTELTDDQAKYLGLNKNGPFKPNYYRY
NTSEQ       1593
              
atgtcgatgcctgacgcgatgccgctgcccggggtcggggaggagctgaagcaggccaag
              
gagatcgaggacgccgagaagtactccttcatggccaccgtcaccaaggcgcccaagaag
              
caaatccagtttgctgatgacatgcaggagttcaccaaattccccaccaaaactggccga
              
agatctttgtctcgctcgatctcacagtcctccactgacagctacagttcagctgcatcc
              
tacacagatagctctgatgatgaggtttctccccgagagaagcagcaaaccaactccaag
              
ggcagcagcaatttctgtgtgaagaacatcaagcaggcagaatttggacgccgggagatt
              
gagattgcagagcaagacatgtctgctctgatttcactcaggaaacgtgctcagggggag
              
aagcccttggctggtgctaaaatagtgggctgtacacacatcacagcccagacagcggtg
              
ttgattgagacactctgtgccctgggggctcagtgccgctggtctgcttgtaacatctac
              
tcaactcagaatgaagtagctgcagcactggctgaggctggagttgcagtgttcgcttgg
              
aagggcgagtcagaagatgacttctggtggtgtattgaccgctgtgtgaacatggatggg
              
tggcaggccaacatgatcctggatgatgggggagacttaacccactgggtttataagaag
              
tatccaaacgtgtttaagaagatccgaggcattgtggaagagagcgtgactggtgttcac
              
aggctgtatcagctctccaaagctgggaagctctgtgttccggccatgaacgtcaatgat
              
tctgttaccaaacagaagtttgataacttgtactgctgccgagaatccattttggatggc
              
ctgaagaggaccacagatgtgatgtttggtgggaaacaagtggtggtgtgtggctatggt
              
gaggtaggcaagggctgctgtgctgctctcaaagctcttggagcaattgtctacattacc
              
gaaatcgaccccatctgtgctctgcaggcctgcatggatgggttcagggtggtaaagcta
              
aatgaagtcatccggcaagtcgatgtcgtaataacttgcacaggaaataagaatgtagtg
              
acacgggagcacttggatcgcatgaaaaacagttgtatcgtatgcaatatgggccactcc
              
aacacagaaatcgatgtgaccagcctccgcactccggagctgacgtgggagcgagtacgt
              
tctcaggtggaccatgtcatctggccagatggcaaacgagttgtcctcctggcagagggt
              
cgtctactcaatttgagctgctccacagttcccacctttgttctgtccatcacagccaca
              
acacaggctttggcactgatagaactctataatgcacccgaggggcgatacaagcaggat
              
gtgtacttgcttcctaagaaaatggatgaatacgttgccagcttgcatctgccatcattt
              
gatgcccaccttacagagctgacagatgaccaagcaaaatatctgggactcaacaaaaat
             gggccattcaaacctaattattacagatactaa
///


> Hey all,
>
> I began writing a program to extract a reaction pathway from
> KEGG/reactome and "transplant" it into another genome, along with all
> of the required genetic 'dependencies' (in the sense of deb/rpm,
> apt/yum dependencies). To do this, I started writing a program that
> would parse KEGG's database format-- here's a reference discussion:
>
> http://groups.google.com/group/diybio/browse_frm/thread/d6ec92a5df6b4e74/3b22b31a504f29ca?#3b22b31a504f29ca
>
> Anyway, at first I thought bioperl hadn't implemented KEGG::Enzyme,
> but now I've noticed that biopython does:
>
> http://www.bioinformatics.org/bradstuff/bp/api/Bio/KEGG/Enzyme/enzyme_format.py.html
> actual implementation:
> http://cvs.biopython.org/cgi-bin/viewcvs/viewcvs.cgi/biopython/Bio/KEGG/Enzyme/Attic/enzyme_format.py?rev=HEAD&cvsroot=biopython&content-type=text/vnd.viewcvs-markup
>
> Have I missed the bioperl implementation of this portion?
>
> Thank you :-).
>
> - Bryan
> http://heybryan.org/
> 1 512 203 0507
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