Conserved pathways within bacteria and yeast

1
Conserved pathways within bacteria and yeast

• ------Something about the Term project for
  Algorithmic Techniques for Biology

2
General

• Given two protein graphs
• Weighted protein relations
• Combine two graphs to one relation graph
• Find a path of length k in the combination graph
  with maximum(minimum) weight.

3
Combining two graphs
G1
G2
a
1
30
2
b
d
20
3
66
c
4
5
5
e
a1
w3
c4
w2
Combination graph
w2
d2
w1
e2
4
Combining graphs

• Each relation become a vertex in combination
  graph.
• Two vertices connected if

2
c
2
2
1
c
c
k
e
4
f
4
e
4
e
c2
c2
c2
W1
W2
W3
e4
e4
e4
5
What we need to do

• Find G1 (Hpylo20040704.tab)
• Find G2 (Scere20040704.tab)
• Find protein relations between G1 and G2
• Combining two graphs
• Find the path in combination graph

6
Where to get data and software

• Get data from http//dip.doe-mbi.ucla.edu/
• Choose Files?SPECIES to get
  Hpylo20040704.tab and Scere20040704.tab
• Choose Files?FASTA to get fasta20040704.seq
  
• (need register to get these files)
• Get software blast fromhttp//www.ncbi.nlm.nih.
  gov/BLAST/
• Choose FAQs? Which BLAST program should I use?
  ?FTP location ftp//ftp.ncbi.nih.gov/blast/execut
  ables/ ? to get such as blast-2.0.10-ia32-win
  32.exe

7
The Format of Hpylo20040704.tab

• DIP4305E DIP3048N PIRB64526 GI2313123 DIP30
  47N SWPO24853 PIRA64520 GI2313078
• DIP4306E DIP3049N SWPO25122 PIRC64564 GI2313
  456 DIP3047N SWPO24853 PIRA64520 GI2313078
• DIP4307E DIP3050N PIRH64618 GI2313921 DIP30
  47N SWPO24853 PIRA64520 GI2313078
• DIP4308E DIP3051N PIRB64520 GI2313079 DIP30
  51N PIRB64520 GI2313079
• DIP4309E DIP3052N SWPP56036 PIRH64669 GI2314
  362 DIP3051N PIRB64520 GI2313079

Edge number
Node number
8
The format of fasta20040704.seq

• gtDIP1NswP19527pirA21762gi112046
• KARMSSLARAELEKRIDSLMDEIAFLKKVHEEEIAELQAQIQYAQISVE
  
• gtDIP2NswpirA23003gi83621
• MKKQNLNSILLMYINYIINYFNNIHKNQLKKDWIMGYEYM
• gtDIP3NswP06778pirA23282gi83448
• MAFLSYFATENQQMQTRRLPRTAEGSGGFGVLLMNEIMDMDEKKPV
• gtDIP4NswP04925pirA23544gi91067
• MANLGYWLLALFVTMWTDVGLCKKRPKPGG

Node number
Protein sequence
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How to get protein relation-1

• Get protein sequence file hp.seq from
  Hpylo20040704.tab and fasta20040704.seq
• DIP4305E DIP3048N PIRB64526 GI2313123 DIP30
  47N SWPO24853 PIRA64520 GI2313078
• DIP4306E DIP3049N SWPO25122 PIRC64564 GI2313
  456 DIP3047N SWPO24853 PIRA64520 GI2313078
• gtDIP3047NswO24853pirA64520gi2313078
• MATRTQARGAVVELLYAFESGNEEIKKIASSMLEEKKIKNNQLA
• gtDIP3048NswpirB64526gi2313123
• MIQIYHADAFEIIKDFYQQNLKVDAIITDPPYNISVKNNFPT
• gtDIP3049NswO25122pirC64564gi2313456
• MKTKAPMKNIRNFSIIAHIDHGKSTLADCLISECNAISNREMKSQVMDT

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How to get protein relation-2

• The format of hp.seq file
• gtDIP3047NswO24853pirA64520gi2313078
• MATRTQARGAVVELLYAFESGNEEIKKIASSMLEEKKIKNNQLAFAL
• gtDIP3048NswpirB64526gi2313123
• MIQIYHADAFEIIKDFYQQNLKVDAIITDPPYNISVKNNFPTLKSAKRQG
  I
• gtDIP3049NswO25122pirC64564gi2313456
• MKTKAPMKNIRNFSIIAHIDHGKSTLADCLISECNA

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How to get protein relation-3

• Get protein sequence file database.seq from
  Scere20040704.tab and fasta20040704.seq in the
  same way with hq.seq.
• Download blast and extract to one directory.
• Copy hp.seq, database.seq to the same dirictory
  with blast

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How to get protein relation-4

• In command mode, go to the blast directory
• Input formatdb -i database.seq -p T -o T to
  make the index file of database.seq
• Input blastall -p blastp -d database.seq -i
  hp.seq -o relation.out to create relation file
  relation.out

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How to get protein relation-5

• The format of relation.out file
• Query DIP3549NswP71408pirE64653gi2314219
• (632 letters)
• Database database.seq
• 4772 sequences 2,345,789 total
  letters
• 
  Score E
• Sequences producing significant alignments
  (bits) Value
• 200_database.seq
  404 e-113
• 276_database.seq
  397 e-111
• 828_database.seq
  184 4e-047
• 2039_database.seq
  182 9e-047
• 1871_database.seq
  177 5e-045
• 4195_database.seq
  176 1e-044

The node number of graph G1
Get node number of G2 from the sequence in
database.seq file
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How to get protein relation-6

• The database.seq file
• gtDIP801NswP29539pirS46157gi626910
• MSKDFSDKKKHTIDRIDQHILRRSQHDNYSNGSSPWMKTNLPPPSPQAH
• gtDIP802NswP39925pirS46611gi626985
• MMMWQRYARGAPRSLTSLSFGKASRISTVKPVLRSRMPVHQRLQTLS
• gtDIP2883NswP33299pirS34354gi422126
• MPPKEDWEKYKAPLEDDDKKPDDDKIVPLTEGDIQVLKSYGAAPYAAK
• gtDIP2884NswQ03656pirS55098gi1078546
• MGSSINYPGFVTKSAHLADTSTDASISCEEATSSQEAKKNFFQRDYNMMK
  K

200 sequence, i.e. row 400.
G2
2039 sequence, i.e. row 4078.
G1
802N
3549N
2883N
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Summary

• Get data Hpylo20040704.tab,Scere20040704.tab
  ,fasta20040704.seq.
• Get sequence file hp.seq, database.seq.
• Get protein relation file relation.out.
• Get combining graph
• Find maximum weighted path of length k in the
  combination graph