not finished pattern for 3B

0:[lvmicyfwa]
1:[rkhdeqnstpg]

3B

[lvmicyfwa][rkhdeqnstpg].{1,4}[rkhdeqnstpg][rkhdeqnstpg].{0,1}[lvmicyfwa].[lvmicyfwa].[lvmicyfwa][rkhdeqnstpga].{1,2}[rkhdeqnstpg].{0,1}[rkhdeqnstpg].[rkhdeqnstpgy].{0,3}[rkhdeqnstpga].{0,2}[lvmicyfwa].[lvmicyfwa].{2,7}[rkhdeqnstpg][rkhdeqnstpg][rkhdeqnstpg].{1,5}[lvmicyfwa][lvmicyfwa].{1,5}[rkhdeqnstpg][rkhdeqnstpg].{0,2}[rkhdeqnstpg].{0,4}[rkhdeqnstpg].{0,1}[rkhdeqnstpga][rkhdeqnstpg].{0,6}[rkhdeqnstpg][lvmicyfwa].{1,8}[rkhdeqnstpg][rkhdeqnstpg].{0,3}[rkhdeqnstpg][lvmicyfwa].[lvmicyfwa].{2}[lvmicyfwa][rkhdeqnstpg].[rkhdeqnstpg][rkhdeqnstpgf].{3}[lvmicyfwag].[lvmicyfwa].[lvmicyfwas].{0,2}[rkhdeqnstpg].[rkhdeqnstpg][rkhdeqnstpg].{0,5}[lvmicyfwa][rkhdeqnstpg].{2,4}[lvmicyfwa].{0,4}[lvmicyfwa]{0,1}

>d1ogae1 b.1.1.1 (E:5-118) T-cell antigen receptor {Human (Homo sapiens), beta-chain}
gitqspkylfrkegqnvtlsceqnlnhdamywyrqdpgqglrliyysqivndfqkgdiaegysvsrekkesfpltvtsaqknptafylcasssrssyeqyfgpgtrltvtedlk

>d1tvda_ b.1.1.1 (A:) T-cell antigen receptor {Human (Homo sapiens), delta-chain}
dkvtqsspdqtvasgsevvllctydtvysnpdlfwyrirpdysfqfvfygddsrsegadftqgrfsvkhiltqkafhlvispvrtedsatyycaftlppptdklifgkgtrvtvep

>d1neu__ b.1.1.1 (-) Myelin membrane adhesion molecule P0 {Rat (Rattus norvegicus)}
ivvytdrevygavgsqvtlhcsfwssewvsddisftwryqpeggrdaisifhyakgqpyidevgtfkeriqwvgdpswkdgsivihnldysdngtftcdvknppdivgktsqvtlyvfe

>d1eaja_ b.1.1.1 (A:) Coxsackie virus and adenovirus receptor (Car), domain 1 {Human (Homo sapiens)}
farslsittpeemiekakgetaylpckftlspedqgpldiewlispadnqkvdqviilysgdkiyddyypdlkgrvhftsndlksgdasinvtnlqlsdigtyqckvkkapgvankkihlvvlv

>d1cdy_1 b.1.1.1 (1-97) CD4 V-set domains {Human (Homo sapiens)}
kkvvlgkkgdtveltctasqkksiqfhwknsnqikilgnqgsfltkspsklndradsrrslwdqgnfpliiknlkiedsdtyicevedqkeevqllv

>d1cid_1 b.1.1.1 (1-105) CD4 V-set domains {Rat (Rattus rattus)}
tsitayksegesaefsfplnlgeeslqgelrwkaekapssqswitfslknqkvsvqkstsnpkfqlsetlpltlqipqvslqfagsgnltltldrgilyqevnlv

>d1hnf_1 b.1.1.1 (4-104) CD2, first domain {Human (Homo sapiens)}
tnaletwgalgqdinldipsfqmsddiddikwektsdkkkiaqfrkeketfkekdtyklfkngtlkikhlktddqdiykvsiydtkgknvlekifdlkiqe

>d1hnga1 b.1.1.1 (A:2-99) CD2, first domain {Rat (Rattus norvegicus)}
dsgtvwgalghginlnipnfqmtddidevrwergstlvaefkrkmkpflksgafeilangdlkiknltrddsgtynvtvystngtrilnkaldlrile

>d1ccza1 b.1.1.1 (A:1-93) CD2-binding domain of CD58, N-terminal domain {Human (Homo sapiens)}
fsqqiygvvygnvtfhvpsnvplkevlwkkqkdkvaelensefrafssfknrvyldtvsgsltiynltssdedeyemespnitdtmkfflyvl

>d1dr9a1 b.1.1.1 (A:1-105) CD80, N-terminal domain {Human (Homo sapiens)}
vihvtkevkevatlscghnvsveelaqtriywqkekkmvltmmsgdmniwpeyknrtifditnnlsivilalrpsdegtyecvvlkyekdafkrehlaevtlsvk

>d1ncna_ b.1.1.1 (A:) CD86 (b7-2), N-terminal domain {Human (Homo sapiens)}
mlkiqayfnetadlpcqfansqnqslselvvfwqdqenlvlnevylgkekfdsvhskymgrtsfdsdswtlrlhnlqikdkglyqciihhkkptgmirihqmnselsvla

>d1f97a1 b.1.1.1 (A:27-128) Junction adhesion molecule, JAM, N-terminal domain {Mouse (Mus musculus)}
kgsvytaqsdvqvpenesikltctysgfssprvewkfvqgsttalvcynsqitapyadrvtfsssgitfssvtrkdngeytcmvseeggqnygevsihltvl

>d1nbqa1 b.1.1.1 (A:25-129) Junction adhesion molecule, JAM, N-terminal domain {Human (Homo sapiens)}
amgsvtvhssepevripennpvklscaysgfssprvewkfdqgdttrlvcynnkitasyedrvtflptgitfksvtredtgtytcmvseeggnsygevkvklivl


http://www.cs.nyu.edu/~ysc212/bioinfo/scop/scoptest/scoptest2.html

48729
48731
48738
48739
48741
48742
48744
48746
48748
48937
48938
63636
89180

1N0X-L
1PEW-A
2CD0-A
1ADQ-L
1W72-L
1NFD-E
1I7Z-B
1DL7-H
1AC6-A
1OGA-E
1TVD-A
1PY9-A
1EAJ-A
1CDY
1CID
1HNF
1HNG-A
1CCZ-A
1QA9-B
1DR9-A
1NCN-A
1F97-A
1NBQ-A
1XE0-A
1OGM-X
1LTO-A
1QFM-A
1H80-A
1WCH-A
1N5M-A
1JIX-A
1JDP-A

pattern for 3A

3A

([lvmicyfwa][rkhdeqnstpg][rkhdeqnstpg].{0,1}[rkhdeqnstpg].{0,1}[lvmicyfwa].{0,3}[rkhdeqnstpg].{0,3}[rkhdeqnstpga][rkhdeqnstpg][rkhdeqnstpg].{0,2}[lvmicyfwa].[lvmicyfwa][rkhdeqnstpga][lvmicyfwa].{2,3}[rkhdeqnstpg][rkhdeqnstpgay].{1,2}[rkhdeqnstpg].{0,1}[rkhdeqnstpg].{0,8}[lvmicyfwagk].[wfliv].{1,2}[rkhdeqnstpg].{0,1}[rkhdeqnstpga].[rkhdeqnstpga].{0,7}[rkhdeqnstpg][lvmicyfwa].{1,9}[rkhdeqnstpg][rkhdeqnstpg][rkhdeqnstpg].{1,2}[rkhdeqnstpga].{0,7}[lvmicyfwa].[lvmicyfwags].{0,4}[rkhdeqnstpgy][rkhdeqnstpga][rkhdeqnstpg].{0,2}[lvmicyfwask][rkhdeqnstpg][lvmicyfwa].[lvmicyfwa].{0,1}[rkhdeqnstpg][rkhdeqnstpg][lvmicyfwa]..[rkhdeqnstpg].{1,2}[ga].[lvmicyfwa].[lvmicyfwa].[lvmicyfwas].{0,1}[rkhdeqnstpg].{0,1}[rkhdeqnstpga].{0,1}[rkhdeqnstpg].{0,2}[rkhdeqnstpg][lvmicyfwa].{3,7}[lvmicyfwa][rkhdeqnstpg])

>d1cd0a_ b.1.1.1 (A:) Immunoglobulin light chain lambda variabledomain, VL-lambda {Human (Homo sapiens), cluster 1}
nfmlnqphsvsespgktvtisctrssgnidsnyvqwyqqrpgsapitviyednqrpsgvpdrfagsidrssnsasltisglktedeadyycqsydarnvvfgggtrltvlg
>d2rhe__ b.1.1.1 (-) Immunoglobulin light chain lambda variable domain, VL-lambda {Human (Homo sapiens), cluster 2}
esvltqppsasgtpgqrvtisctgsatdigsnsviwyqqvpgkapklliyyndllpsgvsdrfsasksgtsaslaisglesedeadyycaawndsldepgfgggtkltvlgqpk
>d1aqkl1 b.1.1.1 (L:1-111) Immunoglobulin light chain lambda variable domain, VL-lambda {Human (Homo sapiens), cluster 3.1}
envltqppsvsgapgqrvtisctgsnsnigagftvhwyqhlpgtapkllifantnrpsgvpdrfsgsksgtsaslaitglqaedeadyycqsydsslsarfgggtrltvlg
>d7fabl1 b.1.1.1 (L:1-103) Immunoglobulin light chain lambda variable domain, VL-lambda {Human (Homo sapiens), cluster 3.2}
asvltqppsvsgapgqrvtisctgsssnigaghnvkwyqqlpgtapkllifhnnarfsvsksgtsatlaitglqaedeadyycqsydrslrvfgggtkltvlr
>d1lgva1 b.1.1.1 (A:1-112) Immunoglobulin light chain lambda variable domain, VL-lambda {Human (Homo sapiens), cluster 4}
etaltqpasvsgspgqsitvsctgvssivgsynlvswyqqhpgkapklltyevnkrpsgvsdrfsgsksgnsasltisglqaedeadyycssydgsstsvvfgggtkltvlg
>d8faba1 b.1.1.1 (A:3-105) Immunoglobulin light chain lambda variable domain, VL-lambda {Human (Homo sapiens), cluster 5}
eltqppsvsvspgqtaritcsanalpnqyaywyqqkpgrapvmviykdtqrpsgipqrfssstsgttvtltisgvqaedeadyycqawdnsasifgggtkltv
>d1nfde1 b.1.1.1 (E:2-107) Immunoglobulin light chain lambda variable domain, VL-lambda {Hamster (Cricetulus griseus)}
yeliqpssasvtvgetvkitcsgdqlpknfaywfqqksdknillliymdnkrpsgiperfsgstsgttatltisgaqpedeaayyclssygdnndlvfgsgtqltvlr
>d1qfoa_ b.1.1.1 (A:) N-terminal domain of sialoadhesin {Mouse (Mus musculus)}
twgvsspknvqglsgscllipcifsypadvpvsngitaiwyydysgkrqvvihsgdpklvdkrfrgraelmgnmdhkvcnlllkdlkpedsgtynfrfeisdsnrwldvkgttvtvtt
>d1nkoa_ b.1.1.1 (A:) N-terminal domain of sialic acid binding Ig-like lectin 7 (SIGLEC-7, p75/AIRM1) {Human (Homo sapiens)}
snrkdysltmqssvtvqegmcvhvrcsfsypvdsdtdsdpvhgywfragndiswkapvatnnpawavqeetrdrfhllgdpqtknctlsirdarmsdagryffrmekgnikwnykydqlsvnvtalt
>d1hkfa_ b.1.1.1 (A:) NK cell activating receptor NKP44 {Human (Homo sapiens)}
aqskaqvlqsvagqtltvrcqypptgslyekkgwckeasalvcirlvtsskprtmawtsrftiwddpdagfftvtmtdlreedsghywcriyrpsdnsvsksvrfylvvs
>d1ie5a_ b.1.1.4 (A:) Neural cell adhesion molecule (NCAM) {Chicken (Gallus gallus)}
gkdiqvivnvppsvrarqstmnatanlsqsvtlacdadgfpeptmtwtkdgepieqedneekysfnydgseliikkvdksdeaeyiciaenkageqdatihlkvfak
>d1cvsc1 b.1.1.4 (C:149-250) Fibroblast growth factor receptor, FGFR {Human (Homo sapiens), FGFR1}
mpvapywtspekmekklhavpaaktvkfkcpssgtpqptlrwlkngkefkpdhriggykvryatwsiimdsvvpsdkgnytciveneygsinhtyqldvver
>d1ev2e1 b.1.1.4 (E:150-250) Fibroblast growth factor receptor, FGFR {Human (Homo sapiens), FGFR2a}
nkrapywtntekmekrlhavpaantvkfrcpaggnpmptmrwlkngkefkqehriggykvrnqhwslimesvvpsdkgnytcvveneygsinhtyhldvve
>d1nunb1 b.1.1.4 (B:151-250) Fibroblast growth factor receptor, FGFR {Human (Homo sapiens), FGFR2b}
krapywtntekmekrlhavpaantvkfrcpaggnpmptmrwlkngkefkqehriggykvrnqhwslimesvvpsdkgnytcvveneygsinhtyhldvve
>d1fltx_ b.1.1.4 (X:) Second domain of the Flt-1 receptor {Human (Homo sapiens)}
grpfvemyseipeiihmtegrelvipcrvtspnitvtlkkfpldtlipdgkriiwdsrkgfiisnatykeiglltceatvnghlyktnylthrqt
>d1kv3a1 b.1.18.9 (A:15-145) Transglutaminase N-terminal domain {Human (Homo sapiens), tissue isozyme}
etngrdhhtadlcreklvvrrgqpfwltlhfegrnyqasvdsltfsvvtgpapsqeagtkarfplrdaveegdwtatvvdqqdctlslqlttpanapiglyrlsleastgyqgssfvlghfillfnawcpa
>d1kv3a2 b.1.5.1 (A:469-585) Transglutaminase, two C-terminal domains {Human (Homo sapiens), tissue isozyme}
eetgmamrirvgqsmnmgsdfdvfahitnntaeeyvcrlllcartvsyngilgpecgtkyllnltlepfseksvplcilyekyrdcltesnlikvrallvepvinsyllaerdlyle



  I've tried the pattern we corrected today on the dataset "ASTRAL SCOP 1.71 with less than 95% identity"
  I think the pattern works pretty good.
 
  The dataset has 13006 sequences.
  The pattern hit 21 sequences as follow.
 
>d1nl0l1 b.1.1.1 (L:1-108) Immunoglobulin light chain lambda variable domain, VL-lambda {Human (Homo sapiens), cluster 2}
qsvltqppsvsaapgqkvtiscsgstsnignnyvswyqqhpgkapklmiydvskrpsgvpdrfsgsksgnsasldisglqsedeadyycaawddslseflfgtgtkltvlg
>d2rhe__ b.1.1.1 (-) Immunoglobulin light chain lambda variable domain, VL-lambda {Human (Homo sapiens), cluster 2}
esvltqppsasgtpgqrvtisctgsatdigsnsviwyqqvpgkapklliyyndllpsgvsdrfsasksgtsaslaisglesedeadyycaawndsldepgfgggtkltvlgqpk
>d1aqkl1 b.1.1.1 (L:1-111) Immunoglobulin light chain lambda variable domain, VL-lambda {Human (Homo sapiens), cluster 3.1}
envltqppsvsgapgqrvtisctgsnsnigagftvhwyqhlpgtapkllifantnrpsgvpdrfsgsksgtsaslaitglqaedeadyycqsydsslsarfgggtrltvlg
>d7fabl1 b.1.1.1 (L:1-103) Immunoglobulin light chain lambda variable domain, VL-lambda {Human (Homo sapiens), cluster 3.2}
asvltqppsvsgapgqrvtisctgsssnigaghnvkwyqqlpgtapkllifhnnarfsvsksgtsatlaitglqaedeadyycqsydrslrvfgggtkltvlr
>d1dcla1 b.1.1.1 (A:1-111) Immunoglobulin light chain lambda variable domain, VL-lambda {Human (Homo sapiens), cluster 4}
psaltqppsasgslgqsvtisctgtssnvggynyvswyqqhagkapkviiyevnkrpsgvpdrfsgsksgntasltvsglqaedeadyycssyegsdnfvfgtgtkvtvlg
>d1lgva1 b.1.1.1 (A:1-112) Immunoglobulin light chain lambda variable domain, VL-lambda {Human (Homo sapiens), cluster 4}
etaltqpasvsgspgqsitvsctgvssivgsynlvswyqqhpgkapklltyevnkrpsgvsdrfsgsksgnsasltisglqaedeadyycssydgsstsvvfgggtkltvlg
>d1adql1 b.1.1.1 (L:2-107) Immunoglobulin light chain lambda variable domain, VL-lambda {Human (Homo sapiens), cluster 5}
yvltqppsvsvapgqtaritcggnnigsksvhwyqqkpgqapvlvvyddsdrppgiperfsgsnsgntatltisrveagdeadyycqvwdsssdhavfgggtkltvlg
>d1w72l1 b.1.1.1 (L:1-107) Immunoglobulin light chain lambda variable domain, VL-lambda {Human (Homo sapiens), cluster 5}
syvltqppsvsvapgqtaritcggnnigsrsvhwyqqkpgqapvlvvyddsdrpsgiperfsgsnsgnmatltisrveagdeadyycqvwdsrtdhwvfgggtdltvlg
>d8faba1 b.1.1.1 (A:3-105) Immunoglobulin light chain lambda variable domain, VL-lambda {Human (Homo sapiens), cluster 5}
eltqppsvsvspgqtaritcsanalpnqyaywyqqkpgrapvmviykdtqrpsgipqrfssstsgttvtltisgvqaedeadyycqawdnsasifgggtkltv
>d1nfde1 b.1.1.1 (E:2-107) Immunoglobulin light chain lambda variable domain, VL-lambda {Hamster (Cricetulus griseus)}
yeliqpssasvtvgetvkitcsgdqlpknfaywfqqksdknillliymdnkrpsgiperfsgstsgttatltisgaqpedeaayyclssygdnndlvfgsgtqltvlr
>d1hxmb1 b.1.1.1 (B:1-123) T-cell antigen receptor {Human (Homo sapiens), delta-chain}
aghleqpqisstktlsktarlecvvsgitisatsvywyrerpgeviqflvsisydgtvrkesgipsgkfevdripetststltihnvekqdiatyycalweaqqelgkkikvfgpgtkliitd
>d1qfoa_ b.1.1.1 (A:) N-terminal domain of sialoadhesin {Mouse (Mus musculus)}
twgvsspknvqglsgscllipcifsypadvpvsngitaiwyydysgkrqvvihsgdpklvdkrfrgraelmgnmdhkvcnlllkdlkpedsgtynfrfeisdsnrwldvkgttvtvtt
>d1nkoa_ b.1.1.1 (A:) N-terminal domain of sialic acid binding Ig-like lectin 7 (SIGLEC-7, p75/AIRM1) {Human (Homo sapiens)}
snrkdysltmqssvtvqegmcvhvrcsfsypvdsdtdsdpvhgywfragndiswkapvatnnpawavqeetrdrfhllgdpqtknctlsirdarmsdagryffrmekgnikwnykydqlsvnvtalt
>d1ie5a_ b.1.1.4 (A:) Neural cell adhesion molecule (NCAM) {Chicken (Gallus gallus)}
gkdiqvivnvppsvrarqstmnatanlsqsvtlacdadgfpeptmtwtkdgepieqedneekysfnydgseliikkvdksdeaeyiciaenkageqdatihlkvfak
>d1fhga_ b.1.1.4 (A:) Telokin {Turkey (Meleagris gallopavo)}
aeekphvkpyftktildmevvegsaarfdckvegypdpevmwfkddnpvkesrhfqidydeegncsltisevcgdddakytckavnslgeatctaellvetm
>d1cvsc1 b.1.1.4 (C:149-250) Fibroblast growth factor receptor, FGFR {Human (Homo sapiens), FGFR1}
mpvapywtspekmekklhavpaaktvkfkcpssgtpqptlrwlkngkefkpdhriggykvryatwsiimdsvvpsdkgnytciveneygsinhtyqldvver
>d1ev2e1 b.1.1.4 (E:150-250) Fibroblast growth factor receptor, FGFR {Human (Homo sapiens), FGFR2a}
nkrapywtntekmekrlhavpaantvkfrcpaggnpmptmrwlkngkefkqehriggykvrnqhwslimesvvpsdkgnytcvveneygsinhtyhldvve
>d1ry7b1 b.1.1.4 (B:150-248) Fibroblast growth factor receptor, FGFR {Human (Homo sapiens), FGFR3c}
apywtrpermdkkllavpaantvrfrcpaagnptpsiswlkngrefrgehriggiklrhqqwslvmesvvpsdrgnytcvvenkfgsirqtytldvler
>d1fltx_ b.1.1.4 (X:) Second domain of the Flt-1 receptor {Human (Homo sapiens)}
grpfvemyseipeiihmtegrelvipcrvtspnitvtlkkfpldtlipdgkriiwdsrkgfiisnatykeiglltceatvnghlyktnylthrqt
>d1kv3a1 b.1.18.9 (A:15-145) Transglutaminase N-terminal domain {Human (Homo sapiens), tissue isozyme}
etngrdhhtadlcreklvvrrgqpfwltlhfegrnyqasvdsltfsvvtgpapsqeagtkarfplrdaveegdwtatvvdqqdctlslqlttpanapiglyrlsleastgyqgssfvlghfillfnawcpa
>d1s4da_ c.90.1.1 (A:) Uroporphyrin-III C-methyltransferase (SUMT, UROM, CobA) {Pseudomonas denitrificans}
faglpalekgsvwlvgagpgdpglltlhaanalrqadvivhdalvnedclklarpgavlefagkrggkpspkqrdislrlvelaragnrvlrlkggdpfvfgrggeealtlvehqvpfrivpgitagigglayagipvthrevnhavtfltghdssglvpdrinwqgiasgspvivmymamkhigaitanliaggrspdepvafvcnaatpqqavlettlaraeadvaaagleppaivvvgevvrlraaldwigaldgrklaadp

http://www.cs.nyu.edu/~ysc212/bioinfo/scop/scoptest/scoptest2.html

88535
88536
88537
88538
88539
88540
88541
88542
48733
89177
89179
49180
49181
81955
49189
63664
74844
88519


1NL0-L
2RHE
1AQK-L
7FAB-L
1DCL-A
1LGV-A
1ADQ-L
1W72-L
8FAB-A
1NFD-E
1HXM-B
1QFO-A
1NKO-A
1IE5-A
1FHG-A
1CVS-C
1EV2-E
1RY7-B
1FLT-X
1KV3-A
1S4D-A

test accuracy from scanprosite

http://www.cs.nyu.edu/~ysc212/bioinfo/scop/scoptest/scoptest2.html
copy paste scanprosite's search result into second box,
it will tell you what's the true positive and false positive.

about false positive and true negative, you should done that when you use scanprosite, not here.
hint: provide true positive pdb code as testing set (Protein(s) to be scanned) on scanprosite, then you can know the true positive rate and false positive rate.

similar rules

http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=2197975

difficulties

difficalty to define strands start and end residuesd1nfde2(see two strands as one or devide into two sheets/domains or delete that strand)

difficalty to decide if a strand should be delete/add or not.1g4m1cf1(how many residues are long enough/ short enough to be add/delete?)(any other way to determin a strand should be add/delete?)

difficalty to define two main sheets1edq (how twisted should be ignored?)(how large/ how small a sheet should be)

difficalty to define a domain1h6e (you can cut both ways)

difficalty to choose two sheets1h6e(if we have more then two sheets, should we delete a sheets or should we devide into two domains?)

there's always something in betweenso, we choose to modify as few as possible while have some consistency.

pattern search

pattern search (seems like no limit)

http://bioportal.cgb.indiana.edu/cgi-bin/emboss/fuzzpro

[arndcqeghilkmfpstwyv]

>d1bwwa_ b.1.1.1 (A:) Immunoglobulin light chain kappa variable domain, VL-kappa {Human (Homo sapiens), cluster 1}
tpdiqmtqspsslsasvgdrvtitcqasqdiikylnwyqqkpgkapklliyeasnlqagv
psrfsgsgsgtdytftisslqpediatyycqqyqslpytfgqgtklqit
>d1eeqa_ b.1.1.1 (A:) Immunoglobulin light chain kappa variable domain, VL-kappa {Human (Homo sapiens), cluster 2}
divltqspdslavslgeratinckssqsvldssnsknylawyqqkpgqppklliywastr
esgvpdrfsgsgsgtdftltisslqaedvavyycqqyyshpysfgqgtkleik


it's not possible to report where is not match in the pattern,
because this is not a correct question.
consider
search 100
in 10110
where is the not-match accord?
usually the question will be, what's the minimal edit distance between two string.
but this question will not work in our case,
because dynamic programming actually list all the possibilities and calculate the 1-to-1 distances for each pair.
and since our case is not compare one string to one string, we compare one string with one pattern, and that pattern can have too many possible sequences.

pattern search algorithms can check here:

Pattern Discovery from Biosequences
ISBN 952-10-0792-3 (paperback)

ISBN 952-10-0819-9(PDF)
http://ethesis.helsinki.fi/julkaisut/mat/tieto/vk/vilo/patternd.pdf

p.67~p.76