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week 4 websites

http://www.umanitoba.ca/faculties/afs/plant_science/courses/39_769/lec06/lec06.1.html

http://www.cs.washington.edu/education/courses/590bi/98w/ppt04/sld001.htm

CLUSTALW

http://workbench.sdsc.edu/

http://www2.ebi.ac.uk/clustalw/

http://www.ddbj.nig.ac.jp/E-mail/clustalw-e.html

http://decypher.stanford.edu/index_by_algo.htm

http://searchlauncher.bcm.tmc.edu/multi-align/multi-align.html

PIMA, MAP

http://dot.imgen.bcm.tmc.edu:9331/multi-align/multi-align.html

MSA

http://workbench.sdsc.edu/

http://dot.imgen.bcm.tmc.edu:9331/multi-align/multi-align.html

BLOCKS

http://blocks.fhcrc.org/blocks/

Blockmaker

http://blocks.fhcrc.org/blocks/

http://dot.imgen.bcm.tmc.edu:9331/multi-align/multi-align.html

Interpro

http://www.ebi.ac.uk/interpro/project_outline.html

InterProScan

http://www.ebi.ac.uk/interpro/scan.html

ProfileScan

http://hits.isb-sib.ch/cgi-bin/PFSCAN

LAMA

http://blocks.fhcrc.org/blocks/help/LAMA_help.html#LAMA

emotif

http://motif.Stanford.EDU/3motif/

http://dna.stanford.edu/emotif/

http://dna.stanford.edu/emotif/database-paper.pdf

Prints

http://www.bioinf.man.ac.uk/dbbrowser/PRINTS/

PROSITE

http://www.expasy.ch/prosite/

PFAM

http://www.sanger.ac.uk/Pfam/

ProDom

http://prodes.toulouse.inra.fr/prodom/2002.1/html/home.php

MEME

http://meme.sdsc.edu/meme/website/

http://bioweb.pasteur.fr/seqanal/motif/meme/

Other motif sites

http://us.expasy.org/tools/#pattern

Clustal query

>gi|1345959|

dwrevwalveaairdgvvrplkctvfhgaqvedafrymaqgkhigkvvvqvlaeepavlkgakpklmsaisktfcpahksyiiagglggfglelaqwliqrgvqklvltsrsgirtgyqakqvrrwrrqglqvqvstsnisslegargliaeaaqlgpvggvfnlavvlrdgllenqtpeffqdvckpkysgtlnldrvtreacpeldyfvvfssvscgrgnagqsnygfansamericekrrheglpglavqwgaigtvgilvetmstndtivsgtlptrigvlglevldlflnqphmvlssfvlaekaaayrdrdsqrdlveavahilgirdlaavnlggsladlgldslmsapvrqt

>gi|11250846|

mnsllvnkaaivtggsrgigfgiaklfaehganvqiwgineeagksaaqdlsdktgskvsfalvdvskndmvsaqvqkflaeygtidvvvnnagitrdsllmrmseeewssvidtnlgsiynvcsavirpmikarsgaivnissivglrgspgqtnyaaakagiigfskalskevgsknirvnciapgfidtdmtkglsdnlknewlkgvplgrvgtpeeiamaalflasnqssyitgqvlsvdggm

>gi|12518153|

msrsvlvtgaskgigraiacqlaadgfnigvhyhrdatgaqetlnaivanggngrllsfdvanreqcrevleheiaqhgawygvvsnagiardaafpalsdddwdavihtnldsfynviqpcimpmigarqggriitlssvsgvmgnrgqvnysaakagiigatkalaielakrkitvnciapglidtgmiemeesalkeamsmipmkrmgqaeevaglasylmsdiagyvtrqvisinggml

>gi|3913638|

mslqgkvalvtgasrgigqaialelgrlgavvigtatsasgaekiaetlkangvegaglvldvssdesvaatlehiqqhlgqplivvnnagitrdnllvrmkddewfdvvntnlnslyrlskavlrgmtkarwgriinigsvvgamgnagqtnyaaakaglegftralarevgsraitvnavapgfidtdmtrelpeaqreallgqiplgrlgqaeeiakvvgflasdgaayvtgatvpvnggmyms

>gi|1084385|

matataagcsgavalkslggrrlcipqqlspvlagfgshaaksfpilstrsiatsgiraqvataekvsagagqsvespvvivtgasrgigkaialslgkagckvlvnyarsskeaeevskeieafggqaltfggdvskeedveamiktavdawgtvdilvnnagitrdgllmrmkksqwqevidlnltgvflctqaaakimmkkkkgriiniasvvglvgnagqanysaakagvigftktvareyasrninvnavapgfissdmtsklgddinkkiletiplgrygqpeevaglveflainpassyvtgqvftidggmtm

>gi|18046|

matataagcsgavalkslggrrlcipqqlspvlagfgshaaksfpilstrsiatsgiraqvataekvsagagqsvespvvivtgasrgigkaialslgkagckvlvnyarsskeaeevskeieafggqaltfggdvskeedveamiktavdawgtvdilvnnagitrdgllmrmkksqwqevidlnltgvflctqaaakimmkkkkgriiniasvvglvgnagqanysaakagvigftktvareyasrninvnavapgfissdmtsklgddinkkiletiplgrygqpeevaglveflainpassyvtgqvftidggmtm

>gi|6459730|

mthneispaparvalvtgssrglgramalrlaqdgftvavhygrgeaeaqqvaadiraaggaaqvfgadlsqpanagtlvedviaalgrldvlvnnagitrdglairmkdedwdavlqtnlssafaacraalkhmmknrsgrivnvssvvalagnpgqanyvaskagligltralakeyggrgitvnaiapgfiesdmtaklpedtkkqyqaniplarfgqpeevaalvaflasegagyitgqtigvdggmnpn

>gi|7430983|

mtaltaqvalvtgasrgigkatalalaatgmkvvvnyaqsstaadavvaeiianggeaiavqanvanadevdqlikttldkfsridvlvnnagitrdtlllrmkledwqavidlnltgvflctkavsklmlkqksgriinitsvagmmgnpgqanysaakagvigftktvakelasrgvtvnavapgfiatdmtenlnaepilqfiplarygqpeevagtirflatdpaaayitgqtfnvdggmvmf

>gi|7431038|

mrkvlitggssglgkriaqiwsqkghqchivgrnefhlketlqslsvakgqqhtltiadvqsdmknlksifesveidtvvhaagvlqsslcvrtsekeidsiictnlvsaiklskmailewfrnknserdrlilnissrlstyalpgtsvyaaskaglesftkvlaaevaskgirvnaispgyvdtpmlssqiraiaekkvpigrlastdeivdactflldnryttgtilpitggl

>gi|7427650|

mnfegkialvtgasrgigraiaetlaargakvigtatsengaqaisdylgangkglmlnvtvmrammkkrhgriitigsvvgtmgnggqanyaaakagligfskslarevasrgitvnvvapgfietdmtralsddqragilaqvpagrlggaqeianavaflasdeaayitgetlhvnggmymv

>gi|2827320|

mrsllhkqalitgggsgiglaiarrlylegcsvtllgrtestlqrasqslllsqplhspaqqpsdtkrvsyhplnvtsasswedllqsnskggkgrvdilincagitqrsplmktsieeveglldtnlrgtvlgckfvgralrnrpsqqhprvkadeggaegvmegteeegkgegkgqgvregvqergviinvasllaqkgvigtsvyaaakagvvglttslaheygrsgirvnavlpgyietdmttglknpsilqqiplgrfgttdevadaalfliknpyanncvlnldgglsav