BIOINFORMATICS WILL
enhance the impact of data
conservation of data
structuring of data into knowledge
change the way we approach problems
open new lines of inquiry
DATABASES ARE TO DATA AS CONSERVATION IS TO ENERGY
HOW WE LOSE DATA:
too many journals, too little library
"obscure" journals
papers not machine-readable
raw data not available
only abstracts are indexed
inconsistent nomenclature
HOW WE CONSERVE DATA
electronic libraries; pay per article
no electronic journal is obscure
electronic papers machine readable
raw data available
entire paper can be indexed
nomenclature stardards; links clarify
relationships
DATA VS. KNOWLEDGE
Knowledge is an informational model consisting of data items and the relationships between them.
knowledge
data item data item data item data item
data item data item
Bioinformatics is the art of encoding biological data into knowledge.
bioinformatics
data
knowledge
URL:
http:/www.genome.ad.jp/htbin/bget_ligand?4.3.1.5
WEB PAGE:
ENTRY EC 4.3.1.5
NAME Phenylalanine ammonia-lyase
CLASS Lyases
Carbon-nitrogen lyases
Ammonia-lyases
SYSNAME L-Phenylalanine ammonia-lyase
REACTION L-Phenylalanine = trans-Cinnamate + NH3
SUBSTRATE L-Phenylalanine
L-Tyrosine
PRODUCT trans-Cinnamate
NH3
trans-4-Hydroxycinnamate
COMMENT This enzyme may also act on L-tyrosine.
PATHWAY PATH: MAP00360 Phenylalanine and tyrosine metabolism (path 2)
PATH: MAP00370 Phenylalanine and tyrosine metabolism (path 3)
MOTIF PS: PS00488 G-[STG]-[LIVM]-[STG]-[AC]-S-G-[DH]-L-x-P-L-[SA]-x(2)-
[SA]
DBLINKS University of Geneva ENZYME DATA BANK: 4.3.1.5
PIR: A24727 A29607 A44133 A56628 JQ1070 JQ2265 PQ0140
S01999 S04127 S04128 S04129 S04463 S06475 S17444
S18352 S20005 S21174 S22991 S25303 S25538 S29029
S48726 S52990 S52991 S52992 S56033
///
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DBGET integrated database retrieval system, GenomeNet (Kyoto center)
FEATURE TABLE:
CDS join(M38619:160..256,M38620:11..307,
M38621:11..179,M38622:11..176,
M38623:11..250,11..103)
/product="green visual pigment"
/gene="G101"
/codon_start=1
RESULTANT SEQUENCE:
>ASYPIGG6:CDS1
atggccgcacacgagcctgtgttcgccgcccggcgccacaatgaagacac
cacaagggagtctgcatttgtctacacaaatgctaataatacaagag
atccttttgaaggaccaaactatcacattgcccctcgatgggtctacaac
gtatcatccttatggatgatctttgttgtcattgcatcagtcttcactaa
tggtttggtaattgtagcaacagcaaagttcaagaagctgcgacaccctc
taaactggattctggtaaacctggctatagccgatctcggggagacagtt
cttgccagcacaatcagtgtcatcaaccagatcttcggctacttcatcct
tggacacccaatgtgcgtttttgaggggtggacggtgtctgtctgtg
gtatcacagctctgtggtctctgactataatctcctgggagcgctgggtg
gttgtgtgcaagccatttggaaatgttaaattcgatggcaaatgggcagc
aggtggcatcatcttctcctgggtttgggccatcatctggtgcacccctc
caatctttggctggagcag
gtactggccccatggtctgaagacatcctgtggccctgatgtgttcagtg
gcagtgaggatccaggagtggcctcctacatgatcaccctaatgcttacc
tgctgtattcttcctctgtccatcattatcatttgctacatttttgtctg
gagtgccatccaccag
gtcgcccagcagcagaaagactcagagtccactcagaaggcagagaagga
agtgtccaggatggtggtagtgatgatccttgcctttattgtgtgctggg
gaccatatgcctcctttgccaccttctctgcagtgaacccaggttatgcc
tggcacccactggcagccgctatgcccgcttacttcgccaagagtgccac
catctacaatcccatcatttacgtcttcatgaaccgccag
ttccggagctgtatcatgcagctgtttggaaagaaggtggaggatgcatc
agaggtttccggctctaccacagaagtttctacagcctcgtaa
CPGN: FEATURE TABLE:
Arabidopsis thaliana
Lhcb1.Ara.tha:1 LHCP AB 165, cab2
Lhcb1.Ara.tha:2 Lhcp2, cab2
Lhcb1.Ara.tha:3 LHCP AB 140, CAB1A, cab1
Lhcb1.Ara.tha:4 Lhb1B1, CAB6P
Lhcb1.Ara.tha:5 Lhb1B2, CAB6P
Cucumus sativus (cucumber)
Lhcb1.Cuc.sat:1 LHCPB
Lhcb1.Cuc.sat:2 LHCPA
Zea mays (maize)
Lhcb1.Zea.may:1 LhCp
Lhcb1.Zea.may:2 Cab-1
Lhcb1.Zea.may:3 LhcabB
Lhcb1.Zea.may:4 cab-ml
Lhcb1.Zea.may:5 zmcab48
SolGenes - Tomato introgression line
[view graphic]
In_introgression_line Z4-,2
Description Lp/Le Introgression Set
Position Map Tomato-4 Ends Left 32.9
Right 40
Drawing Colour BLUE
Label Locus Enzyme Buffer
Contains Pgm-2 None L-TRIS 7.7
TG182 EcoRV
TG146A EcoRV
TG146C EcoRV
TG483 DraI
TG146B EcoRV
TG123 DraI
TG413B EcoRV
Does_not_Contain TG15 EcoRV
TG208 EcoRV
1. Search for EST's from Brassica campestris:
2. Search for EST's from flowers:
3. AND the set.
comm -12 flower@est.nam campestris@est.nam > both.nam
4. Further refinement as above