AlexLabNotebook/ChrIIIRebuild/10/1/05-10/7/05

= 10/1/05 - 10/7/05 =

Last week: 9/24/05-9/30/05

Next week: 10/8/05-10/14/05

Goals this week:
 * Figure out flanking sequences necessary for ncRNA function -- still not done
 * Make initial attempt at using conservation to figure out 5' flanking sequence for genes -- Have conservation data and intergenic regions, need to write code to calculate high-scoring islands
 * Think some more about canonical promoters + using Eran Segal's method -- didn't happen

Canonical promoters

 * Take 5' conserved sequence + specific Pol II promoter with well-identified TATA box etc and use that as promoter in front of all the genes ?
 * Conservation data from Adam Siepel in David Haussler's group. Downloaded conservation scores, will use these to plot score profiles for all the intergenic regions to help figure out which bits of intergenic sequence to include in defining each gene

Visualization

 * Pychart

Intergenic sections of chrIII
Generated by interfeatureregions.py

List of all sections of the chromosome that are in between genes [but may overlap with other elements, like ARS etc], plus 100 bases on either end to show flanking genes:
 * Bases 2035-6579, length: 4544 bases, between YCL076W and YCL073C
 * Bases 8226-9806, length: 1580 bases, between YCL073C and YCL069W
 * Bases 10982-11603, length: 621 bases, between YCL069W and YCL068C
 * Bases 12185-12486, length: 301 bases, between YCL068C and YCL067C
 * Bases 12918-13382, length: 464 bases, between YCL067C and YCL066W
 * Bases 14019-15898, length: 1879 bases, between YCL065W and YCL064C
 * Bases 16780-17390, length: 610 bases, between YCL064C and YCL063W
 * Bases 18461-18916, length: 455 bases, between YCL063W and YCL061C
 * Bases 22006-22529, length: 523 bases, between YCL061C and YCL059C
 * Bases 23279-23623, length: 344 bases, between YCL059C and YCL058C
 * Bases 23825-24132, length: 307 bases, between YCL058W-A and YCL057C-A
 * Bases 24225-24868, length: 643 bases, between YCL057C-A and YCL057W
 * Bases 26806-27025, length: 219 bases, between YCL057W and YCL056C
 * Bases 27259-28029, length: 770 bases, between YCL056C and YCL055W
 * Bases 28836-31549, length: 2713 bases, between YCL055W and YCL054W
 * Bases 33874-34243, length: 369 bases, between YCL054W and YCL052C
 * Bases 35293-35965, length: 672 bases, between YCL052C and YCL051W
 * Bases 37516-37936, length: 420 bases, between YCL051W and YCL050C
 * Bases 38701-39886, length: 1185 bases, between YCL050C and YCL049C
 * Bases 40624-42265, length: 1641 bases, between YCL049C and YCL048W
 * Bases 43456-43761, length: 305 bases, between YCL048W and YCL047C
 * Bases 44337-44723, length: 386 bases, between YCL047C and YCL045C
 * Bases 46863-47211, length: 348 bases, between YCL046W and YCL044C
 * Bases 48264-48753, length: 489 bases, between YCL044C and YCL043C
 * Bases 52240-52745, length: 505 bases, between YCL040W and YCL039W
 * Bases 54782-55041, length: 259 bases, between YCL039W and YCL038C
 * Bases 56427-57474, length: 1047 bases, between YCL038C and YCL037C
 * Bases 58578-59126, length: 548 bases, between YCL037C and YCL036W
 * Bases 60626-60941, length: 315 bases, between YCL036W and YCL035C
 * Bases 61073-61758, length: 685 bases, between YCL035C and YCL034W
 * Bases 62622-62876, length: 254 bases, between YCL034W and YCL033C
 * Bases 63182-63541, length: 359 bases, between YCL033C and YCL032W
 * Bases 64381-64775, length: 394 bases, between YCL032W and YCL031C
 * Bases 65468-66034, length: 566 bases, between YCL031C and YCL030C
 * Bases 68233-68699, length: 466 bases, between YCL030C and YCL029C
 * Bases 69821-70250, length: 429 bases, between YCL029C and YCL028W
 * Bases 71267-71903, length: 636 bases, between YCL028W and YCL027W
 * Bases 73241-73505, length: 264 bases, between YCL027W and YCL026C-B
 * Bases 73886-74804, length: 918 bases, between YCL026C-B and YCL026C-A
 * Bases 75185-76231, length: 1046 bases, between YCL026C-A and YCL025C
 * Bases 77818-79048, length: 1230 bases, between YCL025C and YCL023C
 * Bases 81984-83719, length: 1735 bases, between YCL022C and YCL021W-A
 * Bases 83896-91423, length: 7527 bases, between YCL021W-A and YCL018W
 * Bases 92317-92876, length: 559 bases, between YCL018W and YCL017C
 * Bases 94169-94720, length: 551 bases, between YCL017C and YCL016C
 * Bases 95662-96380, length: 718 bases, between YCL016C and YCL014W
 * Bases 101090-101416, length: 326 bases, between YCL014W and YCL012C
 * Bases 101687-102170, length: 483 bases, between YCL012C and YCL011C
 * Bases 103253-103666, length: 413 bases, between YCL011C and YCL010C
 * Bases 104245-104714, length: 469 bases, between YCL010C and YCL009C
 * Bases 105443-105795, length: 352 bases, between YCL009C and YCL008C
 * Bases 106752-107070, length: 318 bases, between YCL008C and YCL007C
 * Bases 107313-108117, length: 804 bases, between YCL005W-A and YCL005W
 * Bases 108687-109201, length: 514 bases, between YCL005W and YCL004W
 * Bases 110566-110939, length: 373 bases, between YCL004W and YCL002C
 * Bases 111570-112010, length: 440 bases, between YCL002C and YCL001W
 * Bases 112376-113174, length: 798 bases, between YCL001W and YCL001W-A
 * Bases 113435-113864, length: 429 bases, between YCL001W-A and YCL001W-B
 * Bases 113918-115779, length: 1861 bases, between YCL001W-B and YCR001W
 * Bases 115893-117474, length: 1581 bases, between YCR001W and YCR002C
 * Bases 118242-118714, length: 472 bases, between YCR002C and YCR003W
 * Bases 119065-119669, length: 604 bases, between YCR003W and YCR004C
 * Bases 120212-121040, length: 828 bases, between YCR004C and YCR005C
 * Bases 122222-122627, length: 405 bases, between YCR005C and YCR006C
 * Bases 122900-126105, length: 3205 bases, between YCR006C and YCR007C
 * Bases 126624-128564, length: 1940 bases, between YCR007C and YCR008W
 * Bases 130175-130839, length: 664 bases, between YCR008W and YCR009C
 * Bases 131436-132367, length: 931 bases, between YCR009C and YCR010C
 * Bases 133018-133818, length: 800 bases, between YCR010C and YCR011C
 * Bases 136767-137840, length: 1073 bases, between YCR011C and YCR012W
 * Bases 138943-139279, length: 336 bases, between YCR013C and YCR014C
 * Bases 140827-141311, length: 484 bases, between YCR014C and YCR015C
 * Bases 142064-143728, length: 1664 bases, between YCR015C and YCR016W
 * Bases 144400-144867, length: 467 bases, between YCR016W and YCR017C
 * Bases 147528-148332, length: 804 bases, between YCR017C and YCR018C
 * Bases 148797-151702, length: 2905 bases, between YCR018C and YCR018C-A
 * Bases 151756-152931, length: 1175 bases, between YCR018C-A and YCR019W
 * Bases 153822-154106, length: 284 bases, between YCR019W and YCR020C
 * Bases 154553-154924, length: 371 bases, between YCR020C and YCR020C-A
 * Bases 154990-155414, length: 424 bases, between YCR020C-A and YCR020W-B
 * Bases 155450-156201, length: 751 bases, between YCR020W-B and YCR021C
 * Bases 156999-157513, length: 514 bases, between YCR021C and YCR022C
 * Bases 157657-158630, length: 973 bases, between YCR022C and YCR023C
 * Bases 160265-160836, length: 571 bases, between YCR023C and YCR024C
 * Bases 162114-162691, length: 577 bases, between YCR024C and YCR024C-B
 * Bases 162757-163037, length: 280 bases, between YCR024C-B and YCR024C-A
 * Bases 162959-163538, length: 579 bases, between YCR024C-A and YCR025C
 * Bases 163748-164203, length: 455 bases, between YCR025C and YCR026C
 * Bases 166231-167462, length: 1231 bases, between YCR026C and YCR027C
 * Bases 167891-170978, length: 3087 bases, between YCR027C and YCR028C
 * Bases 172316-173042, length: 726 bases, between YCR028C and YCR028C-A
 * Bases 173332-173918, length: 586 bases, between YCR028C-A and YCR030C
 * Bases 176330-177592, length: 1262 bases, between YCR030C and YCR031C
 * Bases 178112-179612, length: 1500 bases, between YCR031C and YCR032W
 * Bases 185915-186581, length: 666 bases, between YCR032W and YCR033W
 * Bases 190061-190684, length: 623 bases, between YCR033W and YCR034W
 * Bases 191527-191926, length: 399 bases, between YCR034W and YCR035C
 * Bases 192910-193389, length: 479 bases, between YCR035C and YCR036W
 * Bases 194190-194506, length: 316 bases, between YCR036W and YCR037C
 * Bases 197077-197713, length: 636 bases, between YCR037C and YCR038C
 * Bases 199310-199638, length: 328 bases, between YCR038W-A and YCR039C
 * Bases 200070-200534, length: 464 bases, between YCR039C and YCR040W
 * Bases 205289-206353, length: 1064 bases, between YCR042C and YCR043C
 * Bases 206536-206969, length: 433 bases, between YCR043C and YCR044C
 * Bases 207842-208227, length: 385 bases, between YCR044C and YCR045C
 * Bases 208993-210006, length: 1013 bases, between YCR045W-A and YCR046C
 * Bases 210315-210810, length: 495 bases, between YCR046C and YCR047C
 * Bases 211399-211963, length: 564 bases, between YCR047W-A and YCR049C
 * Bases 213664-214163, length: 499 bases, between YCR050C and YCR051W
 * Bases 214631-215086, length: 455 bases, between YCR051W and YCR052W
 * Bases 216337-216789, length: 452 bases, between YCR052W and YCR053W
 * Bases 218133-218468, length: 335 bases, between YCR053W and YCR054C
 * Bases 219959-220549, length: 590 bases, between YCR054C and YCR057C
 * Bases 223120-223546, length: 426 bases, between YCR057C and YCR059C
 * Bases 224122-224491, length: 369 bases, between YCR059C and YCR060W
 * Bases 224626-225655, length: 1029 bases, between YCR060W and YCR061W
 * Bases 227350-228187, length: 837 bases, between YCR061W and YCR064C
 * Bases 228683-229402, length: 719 bases, between YCR063W and YCR065W
 * Bases 230896-231592, length: 696 bases, between YCR065W and YCR066W
 * Bases 232855-233217, length: 362 bases, between YCR066W and YCR067C
 * Bases 236214-237306, length: 1092 bases, between YCR067C and YCR068W
 * Bases 238668-239147, length: 479 bases, between YCR068W and YCR069W
 * Bases 239903-240195, length: 292 bases, between YCR069W and YCR071C
 * Bases 240435-240897, length: 462 bases, between YCR071C and YCR072C
 * Bases 242244-242681, length: 437 bases, between YCR072C and YCR073C
 * Bases 246476-247056, length: 580 bases, between YCR073C and YCR073W-A
 * Bases 247803-248126, length: 323 bases, between YCR073W-A and YCR075C
 * Bases 248708-249068, length: 360 bases, between YCR075C and YCR075W-A
 * Bases 249095-249386, length: 291 bases, between YCR075W-A and YCR076C
 * Bases 249938-250331, length: 393 bases, between YCR076C and YCR077C
 * Bases 252521-252938, length: 417 bases, between YCR077C and YCR079W
 * Bases 254066-254464, length: 398 bases, between YCR079W and YCR081W
 * Bases 258544-258976, length: 432 bases, between YCR081C-A and YCR082W
 * Bases 259162-259671, length: 509 bases, between YCR082W and YCR083W
 * Bases 259854-260404, length: 550 bases, between YCR083W and YCR084C
 * Bases 262345-263009, length: 664 bases, between YCR084C and YCR085W
 * Bases 263162-263485, length: 323 bases, between YCR085W and YCR086W
 * Bases 263857-264069, length: 212 bases, between YCR086W and YCR087W
 * Bases 264360-265161, length: 801 bases, between YCR087C-A and YCR088W
 * Bases 266739-267527, length: 788 bases, between YCR088W and YCR089W
 * Bases 272156-272408, length: 252 bases, between YCR089W and YCR090C
 * Bases 272756-274497, length: 1741 bases, between YCR090C and YCR091W
 * Bases 276459-276857, length: 398 bases, between YCR091W and YCR092C
 * Bases 279800-280210, length: 410 bases, between YCR092C and YCR093W
 * Bases 286336-286855, length: 519 bases, between YCR093W and YCR094W
 * Bases 287830-288263, length: 433 bases, between YCR094W and YCR095C
 * Bases 289151-289732, length: 581 bases, between YCR095C and YCR095W-A
 * Bases 289690-293272, length: 3582 bases, between YCR095W-A and YCR096C
 * Bases 293431-293928, length: 497 bases, between YCR096C and YCR097W
 * Bases 294214-294532, length: 318 bases, between YCR097W and YCR097W-A
 * Bases 294598-297142, length: 2544 bases, between YCR097W-A and YCR098C
 * Bases 298498-300925, length: 2427 bases, between YCR098C and YCR099C
 * Bases 302114-302575, length: 461 bases, between YCR100C and YCR101C
 * Bases 302923-304454, length: 1531 bases, between YCR101C and YCR102C
 * Bases 305360-306828, length: 1468 bases, between YCR102C and YCR102W-A
 * Bases 306825-307894, length: 1069 bases, between YCR102W-A and YCR104W
 * Bases 308068-309163, length: 1095 bases, between YCR104W and YCR105W
 * Bases 310048-311051, length: 1003 bases, between YCR105W and YCR106W
 * Bases 313349-313983, length: 634 bases, between YCR106W and YCR107W
 * Bases 314874-316090, length: 1216 bases, between YCR107W and YCR108C