COURSE OF BIOINFORMATICS A.A MULTIPLE SEQUENCE ALIGNMENT (MSA)

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1 COURSE OF BIOINFORMATICS A.A MULTIPLE SEQUENCE ALIGNMENT (MSA) ANTONELLA LISA IGM- CNR PAVIA

2 MSA HAS A SIMPLE DEFINITION: IT IS AN ALIGNMENT THAT CONTAINS MORE THAN TWO SEQUENCES MSA METHODS CAN HANDLE NUCLEOTIDE AS WELL AS AMINO ACIDS SEQUENCES BUT ARE AT THEIR BEST WITH PROTEINS.

3 MULTIPLE ALIGNMENTS ARE ESSENTIAL AND WIDELY USED COMPUTATIONAL PROCEDURES FOR BIOLOGICAL SEQUENCE ANALYSIS. USEFUL TO PREDICT PROTEIN STRUCTURE CENTRAL TO PREDICT THE PROTEIN FUNCTION; TO BUILD GENE/PROTEIN FAMILIES; TO DETERMINE CONSENSUS SEQUENCES CRUCIAL TO RECONSTRUCT PHYLOGENIES

4 MSA CAN BE INTERPRETED AS A REPRESENTATION OF A SET OF SEQUENCES, WHERE: - HOMOLOGOUS RESIDUES ARE ALIGNED IN COLUMNS ACROSS THE LENGTH OF THE SEQUENCES - RESIDUES ARE HOMOLOGOUS IN AN EVOLUTIONARY SENSE OR IN A STRUCTURAL AND/OR FUNCTIONAL SENSE

5 Bioinforma*cs. Vol. 23 no , pp B CONSTRUCTING ACCURATE MSAS IS A COMPUTATIONALLY INTENSE AND BIOLOGICALLY COMPLEX TASK. ALIGNMENT SPEED AND COMPUTATIONAL COMPLEXITY ARE GREATLY AFFECTED WHEN THE NUMBER OF SEQUENCES TO BE ALIGNED INCREASES.

6 EXTENDING THE ALGORITHMS FOR ALIGNMENT BETWEEN 2 SEQUENCES TO K SEQUENCES QUICKLY BECOMES UNREALISTIC DUE TO THE EXPONENTIAL RUNNING TIME REQUIRED FOR 3 SEQUENCES OF LENGTH n, THE RUN TIME SCALES WITH 7n 3 EXAMPLE: ALIGNING 70 GLOBIN GENES OF ~550 BP EACH WE NEED ~ 7.8 X COMPARISONS. ON 1 TERAFLOP MACHINE IT WOULD TAKE ~ 6.0 X YEARS

7 CHOOSING DIFFERENT MSA METHODS MSA METHODS ARE HEURISTIC THESE METHODS REFER TO EXPERIENCE- BASED TECHNIQUES FOR PROBLEM SOLVING THAT FINDS A SOLUTION WHICH IS NOT GUARANTEED TO BE OPTIMAL, BUT GOOD ENOUGH FOR A GIVEN SET OF GOALS. PROGRESSIVE: CLUSTALW/CLUSTAL OMEGA CONSISTENCY BASED: T- COFFEE ITERATIVE: MUSCLE RNA

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9 CLUSTALW ALGORITHM FROM: DAUGELAITE J ET AL. ISRN BIOMATHEMATICS VOLUME 2013 (2013), ARTICLE ID

10 SEQUENCES PAIRWISE ALIGNMENT 1 GUIDED TREE ALL SEQUENCES 2 3 MSA PROGRESSIVE ALIGNMENT OF MOST SIMILAR SEQUENCES MSA THREE- STEPS PROCESS TO RECONSTRUCT A MSA = + = ERRORS MADE IN THE FIRST ALIGNMENTS CANNOT BE RECTIFIED LATER AS THE REST OF THE SEQUENCES ARE ADDED IN.

11 FROM: DAUGELAITE J ET AL. ISRN BIOMATHEMATICS VOLUME 2013 (2013), ARTICLE ID T- COFFEE ALGORITHM TREE- BASED CONSISTENCY OBJECTIVE FUNCTION FOR ALIGNMENT EVALUATION

12 CLUSTAL OMEGA ALGORITHM FROM: DAUGELAITE J ET AL. ISRN BIOMATHEMATICS VOLUME 2013 (2013), ARTICLE ID

13 htp://wiki.bits.vib.be/index.php/exercises_on_mul*ple_sequence_alignment A TOY EXAMPLE EXPLAINING MSA DIFFERENCES ALIGN THE FOLLOWING SEQUENCES USING: CLUSTAL W2 CLUSTAL OMEGA TCOFEE MUSCLE Sequence1: GARFIELDTHELASTFATCAT Sequence2: GARFIELDTHEFASTCAT Sequence3: GARFIELDTHEVERYFASTCAT Sequence4: THEFATCAT Sequence5: GARFIELDTHEVASTCAT

14 htp://wiki.bits.vib.be/index.php/exercises_on_mul*ple_sequence_alignment Sequence1: GARFIELDTHELASTFATCAT Sequence2: GARFIELDTHEFASTCAT Sequence3: GARFIELDTHEVERYFASTCAT Sequence4: THEFATCAT Sequence5: GARFIELDTHEVASTCAT >Sequence1 GARFIELDTHELASTFATCAT >Sequence2 GARFIELDTHEFASTCAT >Sequence3 GARFIELDTHEVERYFASTCAT >Sequence4 THEFATCAT >Sequence5 GARFIELDTHEVASTCAT FASTA Format

15 T- Coffee Mab

16 A PROTEIN SEQUENCE ALIGNMENT (INTEGRIN.TXT) >NP_ integrin beta- 2 precursor [Mus musculus] IQEQSFVIRALGFTDTVTVQVRPQCECQCRDQSREQSLCGGKGVMECGICRCESGYIGKNCECQTQGRSS QELERNCRKDNSSIVCSGLGDCICGQCVCHTSDVPNKEIFGQYCECDNVNCERYNSQVCGGSDRGSCNCG KCSCKPGYEGSACQCQRSTTGCLNARLVECSGRGHCQCNRCICDEGYQPPMCEDCPSCGSHCRDNHTSCA ECLKFDKGPFEKNCSVQCAGMTLQTIPLKKKPCKERDSEGCWITYTLQQKDGRNIYNIHVEDSLECVKGP NVAAIVGGTVVGVVLIGVLLLVIWKALTHLTDLREYRRFEKEKLKSQWNNDNPLFKSATTTVMNPKFAES >NP_ integrin beta- 2 precursor [Homo sapiens] IQEQSFVIRALGFTDIVTVQVLPQCECRCRDQSRDRSLCHGKGFLECGICRCDTGYIGKNCECQTQGRSS QELEGSCRKDNNSIICSGLGDCVCGQCLCHTSDVPGKLIYGQYCECDTINCERYNGQVCGGPGRGLCFCG KCRCHPGFEGSACQCERTTEGCLNPRRVECSGRGRCRCNVCECHSGYQLPLCQECPGCPSPCGKYISCAE CLKFEKGPFGKNCSAACPGLQLSNNPVKGRTCKERDSEGCWVAYTLEQQDGMDRYLIYVDESRECVAGPN IAAIVGGTVAGIVLIGILLLVIWKALIHLSDLREYRRFEKEKLKSQWNNDNPLFKSATTTVMNPKFAES >XP_ integrin beta- 2 isoform X1 [Equus caballus] VQEQSFVIRALGFSDTVTVQVLPQCECQCRDTSPGRSLCRDKGFMECGICRCDTGYIGKNCECQTQGRSS QELEGSCRKDNNSLVCSGLGDCVCGQCICHKSDVPNKEIFGQFCECDNVNCERYDGQVCGGEKRGTCNCG KCQCKEGFEGSACQCPRSTDGCLNQRGTECSGRGRCRCNVCECDDGYQPPLCQDCPGCPSPCGSYISCAE CLKFKKGPYEKTCSVECKNLTLLQEAPSVNRQCKERDSEGCWMTYTLRQRDGMHSYDIHVEDTRECVEGP NIAAIVGGTVAGVVLIGLLLLIVWKALTHLSDLREYKRFEKEKLKSQWNNDNPLFKSATTTVMNPKFAES >NP_ integrin beta- 2 precursor [Ovis aries] NVVELIKSAYNKLSSRVFLDHNTLPDTLKVAYDSFCSNGVSQVDQPRGDCDGVQINVPITFQVKVTATEC IQEQSFTIRALGFTDTVTVRVLPQCECQCREASRDRSVCGGRGSMECGVCRCDAGYIGKNCECQTHGRSS QELEGSCRKDNSSIICSGLGDCICGQCVCHTSDVPNKKIYGQFCECDNVNCERYDGQVCGGDKRGLCFCG TCRCNDQHEGSACQCLKSTQGCLNLDGVECSGRGRCRCNVCQCDPGYQPPLCIDCPGCPVPCAGFAPCTE CLKFDKGPFAKNCSAACGQTKLLSSPVPGGRKCKERDSEGCWMTYTLVQRDGRNRYDVHVDDMLECVKGP

17 INTEGRIN.TXT

18 BEFORE RUNNING A MSA PROGRAM BE SURE OF THE SEQUENCE NAMING NEVER USE SPACES BUT REPLACE THEM WITH THE UNDERSCORE SYMBOL NEVER USE NAME LONGER THAN 15 CHARACTERS NEVER GIVE THE SAME NAME TO TWO DIFFERENT SEQUENCES

19 MSA CONSENSUS SYMBOLS PEEMSVTS-LDLTGGLPEATTPESEEAFTLPLLNDPEPK-PSLEPVKNISNMELKAEPFD! PEEMSVAS-LDLTGGLPEASTPESEEAFTLPLLNDPEPK-PSLEPVKSISNVELKAEPFD! SEELAA--ALDLG----APSPAAAEEAFALPLMTEAPPAVPPKEPSG -SGLELKAEPFD! PGPGPLAEVRDLPG-----STSAKEDGFGWLLPPPPPPP LPFQ! PGPGPLAEVRDLPG-----SAPAKEDGFSWLLPPPPPPP LPFQ!.. : **. :.. *:.* *. * **:! AN ALIGNMENT WILL DISPLAY BY DEFAULT THE FOLLOWING SYMBOLS DENOTING THE DEGREE OF CONSERVATION OBSERVED IN EACH COLUMN: * (ASTERISK) INDICATES POSITIONS WHICH HAVE A SINGLE, FULLY CONSERVED RESIDUE. : (COLON) INDICATES CONSERVATION BETWEEN GROUPS OF STRONGLY SIMILAR PROPERTIES (SCORING > 0.5 IN THE GONNET PAM 250 MATRIX).. (PERIOD) INDICATES CONSERVATION BETWEEN GROUPS OF WEAKLY SIMILAR PROPERTIES (SCORING =< 0.5 IN THE GONNET PAM 250 MATRIX).

20 RESIDUE COLORS ACCORDING TO THEIR PHYSICOCHEMICAL PROPERTIES

21 INTEGRIN.TXT

22 INTEGRIN.TXT

23 JALVIEW IS A FREE PROGRAM FOR MULTIPLE SEQUENCE ALIGNMENT EDITING, VISUALISATION AND ANALYSIS. IT IS USED TO VIEW AND EDIT SEQUENCE ALIGNMENTS, ANALYSE THEM WITH PHYLOGENETIC TREES AND PRINCIPAL COMPONENTS ANALYSIS (PCA) PLOTS AND EXPLORE MOLECULAR STRUCTURES AND ANNOTATION.

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26 EX_01.TXT >beta_homo MVHLTPEEKSAVTALWGKVNVDEVGGEALGRLLVVYPWTQRFFESFGDLSTPDAVMGNPKVKAHGKKVLG AFSDGLAHLDNLKGTFATLSELHCDKLHVDPENFRLLGNVLVCVLAHHFGKEFTPPVQAAYQKVVAGVAN ALAHKYH >beta_equus caballus MVQLSGEEKAAVLALWDKVNEEEVGGEALGRLLVVYPWTQRFFDSFGDLSNPGAVMGNPKVKAHGKKVLH SFGEGVHHLDNLKGTFAALSELHCDKLHVDPENFRLLGNVLVVVLARHFGKDFTPELQASYQKVVAGVAN ALAHKYH >alpha_homo MVLSPADKTNVKAAWGKVGAHAGEYGAEALERMFLSFPTTKTYFPHFDLSHGSAQVKGHGKKVADALTNA VAHVDDMPNALSALSDLHAHKLRVDPVNFKLLSHCLLVTLAAHLPAEFTPAVHASLDKFLASVSTVLTSK YR >alpha_equus MVLSAADKTNVKAAWSKVGGHAGEFGAEALERMFLGFPTTKTYFPHFDLSHGSAQVKAHGKKVGDALTLA VGHLDDLPGALSNLSDLHAHKLRVDPVNFKLLSHCLLSTLAVHLPNDFTPAVHASLDKFLSSVSTVLTSK YR >myoglobin_balaena MVLSDGEWQLVLNIWAKVEADVAGHGQDVLIRLFKGHPETLEKFDKFKHLKTEAEMKASEDLKKHGNTVL TALGGILKKKGHHEAELKPLAQSHATKHKIPIKYLEFISDAIIHVLHSRHPGDFGADAQGAMNKALELFR KDIAAKYKELGFQG >leghaemoglobin [Vigna unguiculata] MVAFSDKQEGLVNGAYEAFKADIPKYSVVFYTTILEKAPAAKNLFSFLANGVDATNPKLTGHAEKLFGLV RDSAAQLRASGGVVADAALGAVHSQKAVNDAQFVVVKEALVKTLKEAVGDKWSDELGTAVELAYDELAAA IKKAY

27 A GOOD MSA CAN BE OBTAINED IF WE CHOOSE THE RIGHT INPUT SEQUENCES. START WITH FEW SEQUENCES (10-15) AND THEN ADD OTHERS AVOID SEQUENCES VERY DIFFERENT OR TOO SIMILAR FROM THE OTHER SEQUENCES OF THE GROUP (<30% OR >80% OF IDENTITY) AVOID SEQUENCES THAT NEED LONG INSERTION/ DELETIONS TO BE PROPERLY ALIGNED

28 HOW TO BE SURE TO GET THE BEST MSA THERE ARE AS MANY GAP- FREE COLUMN AS POSSIBLE THE EXTREMITIES OF YOUR MULTIPLE ALIGNMENT ARE REMOVED THE N- TERMINUS AND THE C- TERMINUS TEND TO BE POORLY CONSERVED THE GAP- RICH REGIONS OF YOUR ALIGNMENT ARE REMOVED INTERNAL, GAP- RICH REGIONS OFTEN CORRESPONDS TO LOOPS. THE MOST INFORMATIVE BLOCKS ARE KEPT DIFFERENT MSAS GIVE SIMILAR RESULTS

29 >Q9ZTS2 MASVSATMISTSFMPRKPAVTSLKPIPNVGEALFGLKSANGGKVTCMASYKVKLITPDGP IEFDCPDNVYILDQAEEAGHDLPYSCRAGSCSSCAGKIAGGAVDQTDGNFLDDDQLEEGWVLTCVAYPQSDV TIETHKEAELVG >Q43517 MASISGTMISTSFLPRKPAVTSLKAISNVGEALFGLKSGRNGRITCMASYKVKLITPEGP IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGSVDQSDGNFLDEDQEAAGFVLTCVAYPKGDV TIETHKEEELTA >Q93XJ9 MASISGTMISTSFLPRKPVVTSLKAISNVGEALFGLKSGRNGRITCMASYKVKLITPDGP IEFECPDDVYILDQAEEEGHDLPYSCRAGSCSSCAGKVTAGTVDQSDGKFLDDDQEAAGFVLTCVAYPKCDV TIETHKEEELTA >P09911 MATTPALYGTAVSTSFLRTQPMPMSVTTTKAFSNGFLGLKTSLKRGDLAVAMASYKVKLVTPDGT QEFECPSDVYILDHAEEVGIDLPYSCRAGSCSSCAGKVVGGEVDQSDGSFLDDEQIEAGFVLTCVAYPTSDV VIETHKEEDLTA >Q7XA98 MATTPALYGTAVSTSFMRRQPVPMSVATTTTTKAFPSGFGLKSVSTKRGDLAVAMATYKVKLITPEGP QEFDCPDDVYILDHAEEVGIELPYSCRAGSCSSCAGKVVNGNVNQEDGSFLDDEQIEGGWVLTCVAFPTSDV TIETHKEEELTA >O04683 MAATTAALSGATMSTAFAPKTPPMTAALPTNVGRALFGLKSSASRGRVTAMAAYKVTLVTPEGK QELECPDDVYILDAAEEAGIDLPYSCRAGSCSSCAGKVTSGSVNQDDGSFLDDDQIKEGWVLTCVAYPTGDV TIETHKEEELTA >P00221 MAATTTTMMGMATTFVPKPQAPPMMAALPSNTGRSLFGLKTGSRGGRMTMAAYKVTLVTPTGN VEFQCPDDVYILDAAEEEGIDLPYSCRAGSCSSCAGKLKTGSLNQDDQSFLDDDQIDEGWVLTCAAYPVSDV TIETHKEEELTA >O04090 MASTALSSAIVGTSFIRRSPAPISLRSLPSANTQSLFGLKSGTARGGRVTAMATYKVKFITPEGE LEVECDDDVYVLDAAEEAGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSFLDDEQIGEGFVLTCAAYPTSDV TIETHKEEDIV >P16972 MASTALSSAIVSTSFLRRQQTPISLRSLPFANTQSLFGLKSSTARGGRVTAMATYKVKFITPEGE QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDDEQMSEGYVLTCVAYPTSDV VIETHKEEAIM >Q93Z60 ARATH/1118 At1g10960/T19D16_12 MASTALSSAIVSTSFLRRQQTPISLRSLPFANTQSLFGLKSSTARGGRVTAMATYKVKFITPEGE QEVECEEDVYVLDAAEEAGLDLPYSCRAGSCSSCAGKVVSGSIDQSDQSFLDD >P27787 FER1_MAIZE/1150 Ferredoxin1, chloroplast precursor MATVLGSPRAPAFFFSSSSLRAAPAPTAVALPAAKVGIMGRSASSRRRLRAQATYNVKLITPEGE VELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADGWVLTCHAYPTSDV VIETHKEEELTGA >O80429 MAIZE/1140 Ferredoxin MAATALSMSILRAPPPCFSSPLRLRVAVAKPLAAPMRRQLLRAQATYNVKLITPEGE VELQVPDDVYILDFAEEEGIDLPFSCRAGSCSSCAGKVVSGSVDQSDQSFLNDNQVADGWVLTCAAYPTSDV VIETHKEDDLL EX_02.TXT FERREDOXIN TRY CLUSTAL OMEGA AND T- COFFEE. DISCUSS THE RESULTS OBTAINED BY THE TWO DIFFERENT MSA.

30 EX_03.TXT > Crassostrea_gigas MATHNFKKSECPSDDTMHALETKEFSIAEFFSKAEFAKLSDYEIKRYMNMRKNYEIMVAVEKKQTVRFSIPVKQSTEKQQ RVTPKKQDHTYLQVGDCEECNKEHEGDCPFHGPLKVIKDVEQPRGISGRAMKTLPQGLFVRDSIIPNAGKGVFAEMCIPK RTRFGPYEGERTENQEEAHETGYAWQIYKHCQRSHFVNAFKEPMSNWMRYVNCARSESEQNLVAFQHRGQIYYRSFKDIL PGTELLVWYGHDYGKELGIFRGEVEIIPKVLNGEEVFCCPFCRMGFSSYEWLSKHCKFKHGEILSKHVPDVKISRQKAVE SEDKSSEMTEKAMEMNQKIGEKPYKCDLCGKSFNLSQHLQKHMRTHTGEKPYKCNVCGKAFNQSQNLQTHMRIHTGEKPY KCNVCGKAFNQSQNLQAHMRTHTGEKPYKCDVCGKAFTESGSLQKHMRTHTGEKPYKCDVCGKAFNQSADLQKHMRIHTG EKPYKCDMCGKAFNQIPHLQTHMRTHTGEKPYKCDVCGKAFNQSADLQKHMRIHTGEKPYKCNMCGKAFNQSQSLQAHKR THTGEKPYKCDVCGKAFSDPSHYRSHKKSHEA >Pteropus_alecto MELPPRHVQSCSELLPESDELLLNVRIRPLDPAQDLVTFEEVVVDFSQEEWALLDPAQKMLYRDVMLENLRNLASVGAGY HLCKHSLITEVEQEELRTEDRSLRGARSVTIMYFLYLSIHMEKNSHKRNESEKAFSQLLFLIQQAPTHPGEKPLEFDHYG KFFRKNCHLICPRYFKGEKCYKYKYGKDFGHRSTLMSHLRTHTGEKILEFNDRGKAFNEEASLRKHLGTPPRENAYEYKQ CLVSFGLHSSFLGHEQIPIGEKLCECSDNGKRSSLSVHKKLCTVEESSKCNEHRKVFTGPLSLQKCARPHTGEKPYECSD CGKAFIFHSSLKKHVRSHTGEKPYKCNHCGKSFSQSSHLTVHKRTHTGEKPYECKECGKAFTVPSSLQKHMRTHTGEKPY ECSDCGKAFIDQSSLKKHRRSHTGEKPYECNQCGKSFSTGSYLIVHKRTHTGEKTYECTECGKAFRNSSCLRVHVRTHTG EKPYKCIQCGKAFSTSTNLIMHKRIHTGQKLYE > Cricetulus_griseus SHLQKHERTHTGEKPYECNQCGKAFSQHSHLQSHKRTHTGEKPYECNQCGKAFAHHNVLQIHKRTHTGEKPYVCNQCGKT FAQHCVLRMHKRTHTGEKPYECNQCGVHLYYVGGEVYVECLSDSSIFVQSRNCNYHHGFHPTTVCKIPSGCSLKIFNNQE FAQILAQSVNHGFETVYELTKMCTIRMSFVKVSSTRLSHSGLTPASPLLFTICISEPSWYIFLSVPSKSTIVQEVVMGT >Mus_musculus MDGTKHCYQYFLCSDSPPFHLRRIKMLKQNTVTYEDVHVNFTQEEWALLDPSQKKLYKGVMLETYRNLNAIGSQSAEKTF EYTQCDKAFILHAHSHAQRRERIDTEKKPHGVIQFFEVFAHYTCLQIQKRPQILKKPYECNQCGKSFANHSNLKRHERTH TGEKCYKCNQCSKAFTNQSRLKRHERIHTGEKPYKCNQCDKAFSQHFYLQTHERIHSGEKPYKCNECDKAYSQLSSLQIH KRTHTGEKPYKCNECSAQAAILKKLP >Cricetulus NPITYDDVHIDFTWKEWTLLDTSQKNLYKDVMLETNKNLTDIGYSREDNTPEDHYTSSRRHERHEGRHTGEKPSAYTQCL KIFAHNSHLQRHKTTHSGGKHYECNQCRKVFASHSKLQMHRRTHTGEKPYECNQCGKAFAQHSHLQIHKRTHTGEKPYAC NQCGKAFSQHSHLQIHKRTHTGEKPYGCNQCGQAFTRHSHLKMHKRRHTGEKPYECIQCGKAFAQHISLQMHEGTHKEQK PYE DISCUSS THE MSA RESULT OBTAINED BY CLUSTAL OMEGA

31 LIST OF MULTIPLE ALIGNMENT RESOURCES 1 MAFFT (TOKYO, JAPAN) MUSCLE AT EBI (HINXTON, UK). CLUSTALW2- CLUSTUL OMEGA AT EBI (HINXTON, UK). DISPLAY AND EDIT ALIGNMENTS WITH JALVIEW. CLUSTALW, MULTALIN AT PBIL (LYON, FRANCE). COLORED ALIGNMENTS AND SECONDARY STRUCTURE PREDICTIONS. CLUSTALW, MAP, PIMA AT BCM (HOUSTON, USA) MSA, CLUSTALW, CTREE AT IBC (ST LOUIS, USA) MULTALIN AT INRA (TOULOUSE, FRANCE). COLORED ALIGNMENTS. CLUSTALW, DCA, DIALIGN2 AT PASTEUR (PARIS, FRANCE) CLUSTALW AT EMBL (HEIDELBERG, GERMANY). PERFORMS MULTIPLE ALIGNMENT ON HOMOLOGOUS SEQUENCES DETECTED BY BLAST. CLUSTALW AT DDBJ (MISHIMA, JAPAN) MAP (MICHIGAN TECH. UNIV., USA) PROBMODEL AT CBRG (ZURICH, SWITZERLAND)

32 LIST OF MULTIPLE ALIGNMENT RESOURCES 2 DIALIGN2 AT BIBISERV (BIELEFELD, GERMANY) DCA AT BIBISERV (BIELEFELD, GERMANY) ITERALIGN (STANFORD, USA) T- COFFEE (LAUSANNE, SWITZERLAND) MATCH- BOX (NAMUR, BELGIUM) BLOCK MAKER AT FHCRC (WASHINGTON, USA) MEME AT SDSC (SAN DIEGO, USA) MEME AT PASTEUR (PARIS, FRANCE) PIMA II AT BMERC (BOSTON, USA) MAVID AT UCB (BERKELEY, USA) CLUSTALW, MAFFT, PRRN AT GENOMENET (KYOTO, JAPAN) BLASTALIGN AT BIOAFRICA (PRETORIA, SOUTH AFRICA) KALIGN AT THE KAROLINSKA INSTITUTE (STOCKHOLM, SWEDEN)

33 MULTIPLE ALIGNMENT EDITORS JALVIEW JAVA MULTIPLE ALIGNMENT EDITOR.(JAVA) CINEMA 2.1 COLOUR INTERACTIVE EDITOR FOR MULTIPLE ALIGNMENTS (JAVA). SEAVIEW (FOR MAC, PC, UNIX AND LINUX COMPUTERS). MPSA (FOR MAC AND UNIX). BELVU (FOR UNIX). SE- AL (FOR MAC). DCSE (FOR UNIX). STRAP (JAVA) GOCORE (MICROSOFT EXCEL) KALIGNVU (WEB- BASED MULTIPLE ALIGNMENT VIEWER)

34 PRETTY PRINTING, SHADING, LOGOS, ETC BOXSHADE (Lausanne, Switzerland) WebLogo (Cambridge, UK) Mview (London, UK) AMAS (Dundee, UK) TEXshade (Tuebingen, Deutschland)