Multiple Sequence Alignment by Parallel Iterative Aligner(KL1,C)

1) Environment

Machine     : Parallel machin based on UNIX
Environment : KLIC,UNIX
Language    : KL1,C
Source Code : 190KB


2) How to install

1.Translation of SourceFiles

  Please copy the program files (./src/*) into the same directory
  on the UNIX file system.

2.Compiling of KL1 and C programs

  Please see ./src/compile.


3) How to use

Put a command as follows.

pia_c_new3 -dp18 -h1m -i100k input_file_name output_file_name

-dp(ProcessingElements)

If you use this program with N Sequences,
-dp(N+1) is best.

If necessary,you can use the options -h and -i.

Please put input_file_name and output_file_name with a absolute path.

--- input_file ( data17 ) ---------------------------------------------------------
[
"KLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLK",
"KLGGGQYGEVYEGVWKKYSLTVAVKTLKEDTMEVEEFLKEAAVMKEIKHPNLVQLLGVCTREPPFYIITEFMTYGNLLDY",
"IGEGEFGEVYRGTLRLPSQDCKTVAIKTLKDTSPGGQWWNFLREATIMGQFSHPHILHLEGVVTKRKPIMIITEFMENGA",
"LLGKGNFGEVYKGTLKDKTSVAVKTCKEDLPQELKIKFLQEAKILKQYDHPNIVKLIGVCTQRQPVYIIMELVSGGDFLT",
"GQGSFGMVYEGNARDIIKGEAETRVAVKTVNESASLRERIEFLNEASVMKGFTCHHVVRLLGVVSKGQPTLVVMELMAHG",
"GSGAFGEVYEGTAVDILGVGSGEIKVAVKTLKKGSTDQEKIEFLKEAHLMSKFNHPNILKQLGVCLLNEPQYIILELMEG",
"GEGAFGKVFLAECHNLLPEQDKMLVAVKALKEASESARQDFQREAELLTMLQHQHIVRFFGVCTEGRPLLMVFEYMRHGD",
"GEGCFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYA",
"GEGEFGKVVKATAFHLKGRAGYTTVAVKMLKENASPSELRDLLSEFNVLKQVNHPHVIKLYGACSQDGPLLLIVEYAKYG",
"GSGAFGTVYKGLWIPEGEKVKIPVAIKELREATSPKANKEILDEAYVMASVDNPHVCRLLGICLTSTVQLITQLMPFGCL",
"VIGKGSFGKVMQVRKKDTQKVYALKAIRKSYIVSKSEVTHTLAERTVLARVDCPFIVPLKFSFQSPEKLYFVLAFINGGE",
"LLGKGTFGQVYQVKKKDTQRIYAMKVLSKKVIVKKNEIAHTIGERNILVTTASKSSPFIVGLKFSFQTPTDLYLVTDYMS",
"LGKGGYGKVFQVRKVTGANTGKIFAMKVLKKAMIVRNAKDTAHTKAERNILEEVKHPFIVDLIYAFQTGGKLYLILEYLS",
"VLGKGSFGKVMLADRKGTEELYAIKILKKDVVIQDDDVECTMVEKRVLALLDKPPFLTQLHSCFQTVDRLYFVMEYVNGG",
"VLGKGNFGKVILSKSKNTDRLCAIKVLKKDNIIQNHDIESARAEKKVFLLATKTKHPFLTNLYCSFQTENRIYFAMEFIG",
"TLGTGSFGRVMLVKHKETGNHYAMKILDKQKVVKLKQIEHTLNEKRILQAVNFPFLVKLEFSFKDNSNLYMVMEYVPGGE",
"LGVGGFGRVELVQLKSEESKTFAMKILKKRHIVDTRQQEHIRSEKQIMQGAHSDFIVRLYRTFKDSKYLYMLMEACLGGE"
].
97.
7.
1.
0.

-----------------------------------------------------------------------------------
Sequences = Alignment Sequences. A List of Strings.
            Strings must be same length.
Cut_ratio = Cut ratio of group_and_group DP(Dynamic Programing) Maching.
U         = First Gap Cost ( U + V )
V         = Second Gap Cost
S         = Out Gap Cost

A Best parameter of Cut_ratio is 90 $B!A(B 97.

Note that writing out a period and a space or a newline character is required
for the input_file to be read in.

--- output_file ( data17.res ) ----------------------------------------------------
"KLGQGCFGEVWMGTWNG--------TTRVAIKTLKPGT-MSPE--AFLQEAQVM---KKL---RHEKLVQLYAVVSE-EPIYIVTEYMSKGSLLDFLK"
"KLGGGQYGEVYEGVWKK-------YSLTVAVKTLKE---DTMEVEEFLKEAAVM---KEI---KHPNLVQLLGVCTREPPFYIITEFMTYGNLLDY--"
"-IGEGEFGEVYRGTLRL----PSQDCKTVAIKTLKDTS-PGGQWWNFLREATIM---GQF---SHPHILHLEGVVTKRKPIMIITEFMENGA------"
"LLGKGNFGEVYKGTLKD--------KTSVAVKTCKEDL-PQELKIKFLQEAKIL---KQY---DHPNIVKLIGVCTQRQPVYIIMELVSGGDFLT---"
"--GQGSFGMVYEGNARDII--KGEAETRVAVKTVNESA-SLRERIEFLNEASVM---KGF---TCHHVVRLLGVVSKGQPTLVVMELMAHG-------"
"--GSGAFGEVYEGTAVDIL-GVGSGEIKVAVKTLKKGS-TDQEKIEFLKEAHLM---SKF---NHPNILKQLGVCLLNEPQYIILELMEG--------"
"--GEGAFGKVFLAECHNLL--PEQDKMLVAVKALKEA--SESARQDFQREAELL---TML---QHQHIVRFFGVCTEGRPLLMVFEYMRHGD------"
"--GEGCFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDA-TEKDLSDLISEMEMM---KMIG--KHKNIINLLGACTQDGPLYVIVEYA----------"
"--GEGEFGKVVKATAFHLK--GRAGYTTVAVKMLKENA-SPSELRDLLSEFNVL---KQV---NHPHVIKLYGACSQDGPLLLIVEYAKYG-------"
"--GSGAFGTVYKGLWIPE---GEKVKIPVAIKELREAT-SPKANKEILDEAYVM---ASV---DNPHVCRLLGICLT-STVQLITQLMPFGCL-----"
"VIGKGSFGKVMQVRKKD-----TQKVYALKAIRKSYIV-SKSEVTHTLAERTVL---ARV---DCPFIVPLKFSFQSPEKLYFVLAFINGGE------"
"LLGKGTFGQVYQVKKKD-----TQRIYAMKVLSKKVIV-KKNEIAHTIGERNIL---VTTASKSSPFIVGLKFSFQTPTDLYLVTDYMS---------"
"-LGKGGYGKVFQVRKVTGA--NTGKIFAMKVLKKAMIVRNAKDTAHTKAERNIL---EEV---KHPFIVDLIYAFQTGGKLYLILEYLS---------"
"VLGKGSFGKVMLADRKG-----TEELYAIKILKKDVVI-QDDDVECTMVEKRVL---ALLD--KPPFLTQLHSCFQTVDRLYFVMEYVNGG-------"
"VLGKGNFGKVILSKSKN-----TDRLCAIKVLKKDNII-QNHDIESARAEKKVFLLATKT---KHPFLTNLYCSFQTENRIYFAMEFIG---------"
"TLGTGSFGRVMLVKHKE-----TGNHYAMKILDKQKVV-KLKQIEHTLNEKRIL---QAV---NFPFLVKLEFSFKDNSNLYMVMEYVPGGE------"
"-LGVGGFGRVELVQLKS----EESKTFAMKILKKRHIV-DTRQQEHIRSEKQIM---QGA---HSDFIVRLYRTFKDSKYLYMLMEACLGGE------"
Score = -12450
Count = 23
[','(2026,12),','(1152,5),','(117,3),','(-1175,1),','(-2442,4),','(-3955,8),','(-5686,7),','(-7000,0),','(-7853,9),','(-8609,6),','(-9329,2),','(-10037,11),','(-10899,14),','(-11641,13),','(-12275,16),','(-12318,12),','(-12335,1),','(-12356,3),','(-12370,2),','(-12394,0),','(-12410,9),','(-12435,8),','(-12450,1)]

-----------------------------------------------------------------------------------
Result = Alignment Result.
Score  = Result Score.
Count  = Total counts of the iterative strategy.
         Selected counts of group_and_group DP Maching in Iterative Aligner.
Path   = Records of selected group_and_group DP Maching in Iterative Aligner.
         List.
