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Part 1 - CpG island prediction

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    Cpg islands were predicted using the Purdue EMBOSS server. 

     

    CPGPLOT islands of unusual CG composition
    sequence_2 from 1 to 150000
    
         Observed/Expected ratio > 0.60
         Percent C + Percent G > 50.00
         Length > 200
    
     Length 293 (372..664)
    
     Length 290 (672..961)
    
     Length 723 (1091..1813)
    
     Length 320 (2530..2849)
    
     Length 662 (3516..4177)
    
     Length 589 (4277..4865)
    
     Length 246 (10178..10423)
    
     Length 299 (10602..10900)
    
     Length 606 (12157..12762)
    
     Length 408 (14151..14558)
    
     Length 370 (20879..21248)
    
     Length 862 (21570..22431)
    
     Length 534 (22582..23115)
    
     Length 215 (27360..27574)
    
     Length 1409 (29207..30615)
    
     Length 285 (32078..32362)
    
     Length 2378 (32701..35078)
    
     Length 1073 (35134..36206)
    
     Length 944 (39763..40706)
    
     Length 1277 (41349..42625)
    
     Length 2629 (42701..45329)
    
     Length 1122 (45385..46506)
    
     Length 418 (46626..47043)
    
     Length 843 (47069..47911)
    
     Length 284 (48201..48484)
    
     Length 3278 (48500..51777)
    
     Length 454 (51779..52232)
    
     Length 1058 (52254..53311)
    
     Length 1148 (53377..54524)
    
     Length 345 (54619..54963)
    
     Length 263 (55405..55667)
    
     Length 1231 (56052..57282)
    
     Length 399 (58540..58938)
    
     Length 328 (59126..59453)
    
     Length 202 (61505..61706)
    
     Length 443 (62173..62615)
    
     Length 346 (71424..71769)
    
     Length 354 (73406..73759)
    
     Length 286 (79668..79953)
    
     Length 204 (80963..81166)
    
     Length 404 (81416..81819)
    
     Length 338 (84690..85027)
    
     Length 316 (87089..87404)
    
     Length 560 (91331..91890)
    
     Length 202 (93347..93548)
    
     Length 212 (98204..98415)
    
     Length 734 (99739..100472)
    
     Length 305 (102041..102345)
    
     Length 485 (102922..103406)
    
     Length 299 (109409..109707)
    
     Length 299 (110673..110971)
    
     Length 267 (113086..113352)
    
     Length 1215 (114190..115404)
    
     Length 343 (115760..116102)
    
     Length 405 (117884..118288)
    
     Length 396 (118293..118688)
    
     Length 547 (119231..119777)
    
     Length 203 (121085..121287)
    
     Length 205 (125299..125503)
    
     Length 210 (125598..125807)
    
     Length 241 (125960..126200)
    
     Length 560 (127401..127960)
    
     Length 315 (128121..128435)
    
     Length 1060 (128477..129536)
    
     Length 2740 (129562..132301)
    
     Length 645 (132396..133040)
    
     Length 2038 (133072..135109)
    
     Length 762 (135307..136068)
    
     Length 200 (136128..136327)
    
     Length 349 (137286..137634)
    
     Length 767 (137656..138422)
    
     Length 713 (138507..139219)
    
     Length 297 (139239..139535)
    
     Length 973 (139553..140525)
    
     Length 1197 (140611..141807)
    
     Length 362 (141829..142190)
    
     Length 343 (143915..144257)

    cpgplot.1.png

    Augustus_graphical.png

    We can see from the AUGUSTUS graphical output that the CpG islands pretty much line up with the output for gene prediction using AUGUSTUS.

     

    Also using EMBOSS, list of inverted repeats - Outfile.txt


    kpadmana 11 October 2012

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