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Sequence Isolation from Scaffold Database Using p450 and hits against 454 Database

Isolate sequence fragments from scaffolds using p450 hits against the 454 database. Align the isolated sequences with EST to analyze genetic data efficiently. Explore sequence variation and gene expression patterns.

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Sequence Isolation from Scaffold Database Using p450 and hits against 454 Database

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  1. p450 hits against 454 database

  2. Isolate the sequence from scaffolds >scaffold02252|4452:4790|CYP51G2|2e-40 ACGTGGCCGGTCTTCGGCGGGTTAATCCGGTTCctAAAAGGaCCGGTTGTGATGCTAAGAGAAGAGTACCCGAAACTAGGGAGTGTGTTCACGTTGAACTTGTTCAACAAAAAGATCACTTTCTTTATCGGGCCTGAGGTTTCAGTCCATTTCTTTAAAGCTTCTGAATCTAATCTGAGCCAACAAGAAGTGTACAAGTACATTGTGCCTACCTTTGGGCCCGGAGTGATTTACGATGTTGATTATAGCGTACGGCAGGAGCAGTTTCGGTTCTTTACTGAGAGTCTAAGGGTTAACAAGTTGAAAGGTTATGTGGGTCAGATGCTTATTGAAGCTCA >scaffold02252|8063:8362|CYP51G2|8e-35 TCGCCTGCTTTCGCTAATCgTCTCCCTCATATATTCAAGGATCCGGACACGTTTGACCCTGACAGATTTGCTCCCGGTAGGGAagAAGACAAAGTGTCTGGGGCgTTttCGTACATCTCTTTTGGCGGTGGCAGGCACGCGTGTCTAGGGGAGCCGTTCGCGTATCTGCAAATAAAATCgATTTGGAGCCATTTGCTGAGGAACTTTGAGCTGGAACTGGTTTCACCTTTTCCGGAGATTGACTGGAATGCCATGGTCGTGGGTGTGAAAGGAAaGgTTATGGTGCGGTACAAGCGCCG >scaffold06866|14030:14566|CYP51G2|6e-16 ACTGAATCTTTTTGTACTTCCAAATTACAGGACATGTTtGTGGGAGGAaCTGATACAACCTCAGCAACCATGGAGTGGGCAATGGCAGAGCTGATGAAAAaTCCAACAAaGATgAaGAAAGCTCAAAAaGAGGTGCGAAGAGTGGTTGGGAAAAAaTCCAAGAtcAGTCAAGATGATATTGCTCAAATGGAATACTTAAAaTGTGTTGTCAAAGAgACTCTTAGATTACATCCTCCAGCTCCTTTTTtGGTtCCTAGAGAATTGACTGAGAGTACTACATTGGAAGGCTATGATATTCCTCCAAAAaCAAGAATATTCATTAATGCATGGGCAATTCAAAGagATTCCAAATACTGGGACCAGCCAGAAGAATTCcTTCCAGAGAGATTtGCTAACAACTTGGTTGATTTtAGAGGCCAAGAcTTCCAaTTCATTCCATTTGGAGCAGGGCgAAGGGGCTGTCCTGGCATTTCATTTGGTGTCATGGAAGTTGAACTTGTACTTGCCAACCTCTTGTACTGGTTTGACTGGAAGTT >scaffold06866|9256:9750|CYP51G2|6e-15 GCAGGAACTGATACAACTTCAACAACCTtAGAGTGGGCAATGGCAGAGCTAATGAAAAGTCCAACTAGGATGAAGAAAaTtCAAGAaGAGGTACGAAGaGTGGTtGGgAAGAAaTCCAAGATCAATCAAgaTGATATtGATCAAATGgACTACTTAAAATGTGTTGTCAAAGAGACTCTTAGATTACATCCTCCAGGTCCTTTTTtGGTtCCTAGAGAATCAAGTGAGAGTACTAAATTGGGAGGTTATGATATTCCTCCAAAAACAAGAATTTTCATCAATGTTTGGGCAATTCAAAGAGATCCCAAATACTGGGATAGGCCCGAAGAATTTCTTCCAGAGAGATTTGCTAACAACCCGATTGATTTtAAAGGCAAAGACTTCGAATTCATCCCATTTGGTGCAGGGCGAAGGGGCTGTCCTGGAATTTCATTTGCAATCACTGAAACTGAACAAGTGCTTGCCAATCTCTTGTACTGGTTTGATTGGAAGTT

  3. Align isolated sequences with EST >scaffold02252|4452:4790|CYP51G2|2e-40 ACGTGGCCGGTCTTCGGCGGGTTAATCCGGTTCctAAAAGGaCCGGTTGTGATGCTAAGAGAAGAGTACCCGAAACTAGGGAGTGTGTTCACGTTGAACTTGTTCAACAAAAAGATCACTTTCTTTATCGGGCCTGAGGTTTCAGTCCATTTCTTTAAAGCTTCTGAATCTAATCTGAGCCAACAAGAAGTGTACAAGTACATTGTGCCTACCTTTGGGCCCGGAGTGATTTACGATGTTGATTATAGCGTACGGCAGGAGCAGTTTCGGTTCTTTACTGAGAGTCTAAGGGTTAACAAGTTGAAAGGTTATGTGGGTCAGATGCTTATTGAAGCTCA Query= scaffold02252|8063:8362|CYP51G2|8e-35 > Contig9662 Query 4 CCTGCTTTCGCTAATCGTCTCCCTCATATATTCAAGGATCCGGACACGTTTGACCCTGAC 63 ||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||| Sbjct 582 CCTGCTTTCGCTAATCGTCTCCCTCATATTTTCAAGGATCCGGACACGTTTGACCCTGAC 641 Query 64 AGATTTGCTCCCGGTAGGGAAGAAGACAAAGT-GTCTGGGGCGTTTTCGTACATCTCTTT 122 ||||||||||||||||| |||||||||||||| | ||||||| ||||||||||||||||| Sbjct 642 AGATTTGCTCCCGGTAGAGAAGAAGACAAAGTAG-CTGGGGCATTTTCGTACATCTCTTT 700 Query 123 TGGCGGTGGCAGGCACGCGTGTCTAGGGGAGCCGTTCGCGTATCTGCAAATAAAATCGAT 182 ||| ||||||||||||| |||| |||||||||| || || ||||||||||||||| | || Sbjct 701 TGGTGGTGGCAGGCACGGGTGTTTAGGGGAGCCTTTTGCTTATCTGCAAATAAAAGCCAT 760 Query 183 TTGGAGCCATTTGCTGAGGAACTTTGAGCTGGAACTGGTTTCACCTTTTCCGGAGATTGA 242 ||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||| Sbjct 761 TTGGAGCCATTTGCTGAGGAATTTTGAGCTGGAACTGGTCTCACCTTTTCCGGAGATTGA 820 Query 243 CTGGAATGCCATGGTCGTGGGTGTGAAAGGAAAGGTTATGGTGCGGTACAAGCG 296 |||||||||||||||||||||||||||||||||||||||||||||||||||||| Sbjct 821 CTGGAATGCCATGGTCGTGGGTGTGAAAGGAAAGGTTATGGTGCGGTACAAGCG 874

  4. Issues/Frustrations • >scaffold07086|5306:4950|CYP51G2|6e-45 • Could not find good software… • JCVI, Washington University Genome Center • Blast has “tool” to isolate… poor documentation • Artemis stinks

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