Jobim08

Hello,

I want to use "Bio::Tools::Run::Phrap - a wrapper for running Phrap" package (for Windows system), could you please let me know how can I use it and I have to install Phrap package or not?

For example, I have two sequence files (read1 and read2) and I want to have two corresponding contigs. How can I do for get it? Is there a way to run two files in the same Perl's program?

The same question for "Bio::Tools::Run::Cap3 - wrapper for Cap3" and for "Bio::Tools::Alignment::Consed - A module to work with objects from consed .ace files".

Thank you in advance! Trang

read1

>R1 AGCCGGTACCCAGTTTTAGTTTTCCTCTGAAGCAAGCACACCTTCCCTTTCCCGTCTGTCTATCCATCCCTGACCCTGTT GTCTGTCTATCCCTGACCCCGTAGTCTCCTAAGTCGCCCCAGATTTTGTGAACACCCTCTGGAACTAGAATCTAGTGGGC GGATGGACCATTTACTAGACGGAGGTAGAGGTGGGTGGATGCGACGACAGGGTGCATAGTCAGCCCGGTTTTAAGGGCAG GTCACTTGGTAGGTCAGCAGGCGGGTCAGTGGGCGGGTGCCTGCAGCATTTATGAACTTATTTGGCCCAGCAAACATTTT GAGTGTCAGGCCGTGCCTACCCAAGGTGAGGGTAAGGAGCAAAATCAGCCCAGCCCAGAGCACTGGGTGGCTACACAGAG CCGACCTCTAATGTGCGCTCCGGGTCGGGATGGCACTCAGCTCGCCTTTAGGGAGTGATGATCTGGATGCCTGGCTTGGA GGTGACAGAGCCTGCCCTTATGAGACAATTAAGAGACTGACTAAGCACCCGGCAGGAGGCCACGAGAATCCCCATGTGAG AAAGAAGAGCATAAACAGGAAACACATTTAATAATTAAACAAAGATAACTCCCTCGTGTGCGCGCACCGGGCCAGCCCCT ATAGAAACATCTGAGGAGTCACTTCCTCCCATGACTCTCGCCCGCCCGGCCGGCTGGAGTCGGCTCCTGGCAAGCTTCAG GCACCTCAGTTGTCCTGAATACACACAGCACCCTTTCCTTACTGAAGCCCCTGAGAGCCTCCAGTTCTCCCTCCTTGCTC ACCCACACTTCCTCCCTCCCGGCCCCTTCAGCGTTCCCAAAGGTAAATGTGGGCTGGGAG >R2 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGTTTTAGTTTTCCTCTGAAGCAAGC ACACCTTCCCTTTCCCGTCTGTCTATCCATCCCTGACCCTGTTGTCTGTCTATCCCTGACCCCGTAGTCTCCTAAGTCGC CCCAGATTTTGTGAACACCCTCTGGAACTAGAATCTAGTGGGCGGATGGACCATTTACTAGACGGAGGTAGAGGTGGGTG GATGCGAAGCACAGGGTGCATAGTCAGCCCGGTTTTAAGGGCAGGTCACTTGGTAGGTCAGCAGGCGGGTCAGTGGGCGG GTGCCTGCAGCATTTATGAACTTATTTGGCCCAGCAAACATTTTGAGTGTCAGGCCGTGCCTACCCAAGGTGAGGGTAAG GAGCAAAATCAGCCCAGCCCAGAGCACTGGGTGGCTACACAGAGCCGACCTCTAATGTGCGCTCCGGGTCGGGATGGCAC TCAGCTCGCCTTTAGGGAGTGATGATCTGGATGCCTGGCTTGGAGGTGACAGAGCCTGCCCTTATGAGACAATTAAGAGA CTGACTAAGCACCCGGCAGGAGGCCACGAGAATCCCCATGTGAGAAAGAAGAGCATAAACAGGAAACACATTTAATAATT AAACAAAGATAACTCCCTCGTGTGCGCGCACCGGGCCAGCCCCTATAGAAACATCTGAGGAGTCACTTCCTCCCATGACT CTCGCCCGCCCGGCCGGCTGGAGTCGGCTCCTGGCAAGCTTCAGGCACCTCAGTTGTCCTGAATACACACAGCACCCTTT CCTTACTGAAGCCCCTGAGAGCCTCCAGTTCTCCCTCCTTGCTCACCCAGACTTCCTCCCTCCCGGCCCCTTCAGCGTTC CAAAGGGTAAATGTGGGCTGGGAAGACAGCTCAGCAGTGGAGAAATCGGGGTGCAGGTCAGTTGCTGCATAGACACACAG GTACACACACATTATTCAAAATTAAAAAAAGAAAAACCAACAGGTTTCTTTGGGTTGAGGCC

read2

>R3 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNAGTTTTAGTTTTCCTCTGAAGCAAGC ACACCTTCCCTTTCCCGTCTGTCTATCCATCCCTGACCCTGTTGTCTGTCTATCCCTGACCCCGTAGTCTCCTAAGTCGC CCCAGATTTTGTGAACACCCTCTGGAACTAGAATCTAGTGGGCGGATGGACCATTTACTAGACGGAGGTAGAGGTGGGTG GATGCGAACGACAGGGTGCATAGTCAGCCCGGTTTTAAGGGCAGGTCACTTGGTAGGTCAGCAGGCGGGTCAGTGGGCGG GTGCCTGCAGCATTTATGAACTTATTTGGCCCAGCAAACATTTTGAGTGTCAGGCCGTGCCTACCCAAGGTGAGGGTAAG GAGCAAAATCAGCCCAGCCCAGAGCACTGGGTGGCTACACAGAGCCGACCTCTAATGTGCGCTCCGGGTCGGGATGGCAC TCAGCTCGCCTTTAGGGAGTGATGATCTGGATGCCTGGCTTGGAGGTGACAGAGCCTGCCCTTATGAGACAATTAAGAGA CTGACTAAGCACCCGGCAGGAGGCCACGAGAATCCCCATGTGAGAAAGAAGAGCATAAACAGGAAACACATTTAATAATT AAACAAAGATAACTCCCTCGTGTGCGCGCACCGGGCCAGCCCCTATAGAAACATCTGAGGAGTCACTTCCTCCCATGACT CTCGCCCGCCCGGCCGGCTGGAGTCGGCTCCTGGCAAGCTTCAGGCACCTCAGTTGTCCTGAATACACACAGCACCCTTT CCTTACTGAAGCCCCTGAGAGCCTTCAGTTCGTCCTCCTTGCTTCACCACACTTTCCTCCTTCCGGGCCCCTTCAGCGTT CCAAAGGGGAAATTGTGGGCTGGGAAGACAGCTCACCA >R4 CGATTCAGCTCGGTACCAATGTGATATGTATATAATATATAATATGCAATATATAAAGAATATGTAACTCTTTAATATCT GTGTGTATATATACATATATACACACACACACATATGTGGTNNGTGTGTGTCTGTGTGTGTGTGTTCTTTAAAATTTTTG CCAGGCACGATGGTACACACCTTTAATCCTAGCACTTGGGAGACAGAGGCATGTGGATCTCTATGAGTTCTAGGCCAGTC AATGCTACATAATGAGTCTTTATCTCAAAGAAACTGTTGGTTTTTTTTTTTTTTAATTTTGTATATGTGTGTGTACCTGT GTGTCTATGCAGCAACTGACCTGCACCCCGATTTCTCCACTGCTGAGCTGTCTTCCCAGCCCACATTTACCCTTTGGAAC GCTGAAGGGGCCGGGAGGGAGGAAGTGTGGGTGAGCAAGGAGGGAGAACTGGAGGCTCTCAGGGGCTTCAGTAAGGAAAG GGTGCTGTGTGTATTCAGGACAACTGAGGTGCCTGAAGCTTGCCAGGAGCCGACTCCAGCCGGCCGGGCGGGCGAGAGTC ATGGGAGGAAGTGACTCCTCAGATGTTTCTATAGGGGCTGGCCCGGTGCGCGCACACGAGGGAGTTATCTTTGTTTAATT ATTAAATGTGTTTCCTGTTTATGCTCTTCTTTCTCACATGGGGATTCTCGTGGCCTCCTGCCGGGTGCTTAGTCAGTCTC TTAATTGTCTCATAAGGGCAGGCTCTGTCACCTCCAAGCCAGGCATCCAGATCATCACTCCCTAAAGGCGAGCTGAGTG >R5 NNCCGGGGGCGCCCGGATGCTTAATTAAGTCTAGATCGTTGAAACGTCATAGCAATATATTAAGAATATGTAACTCTTTA ATATCTGTGTGTATATATACATATATACACACACACGACATATGTGTGGTAGATAGGTTGATATACTGTGTTGTGTGTGG TCTTTAAAATTTTTGGCATGCACGATGGTACACACCTATGATCCGAGCACTTGGGAGACAGAGGCATGTGGAGCTCTATG AGTTCTAGGCCAGTCAATGCTACATAATGAGTCTTTATCTCAAAGAAACTGGTGGTATGTTTATTTTATAATTTTGTATA TGTGTGTGTACCTGTGTGTCTATACAGCGACTGATTCTGCACCCCGGTGTCTCCACTGCTGAGCTGGCTTCCCAGCCCAC ATTTACCCTTTGGAACTCTGAGGGGGCCGGGATGGAGGTATTGTGTGGGAACGTGTAGGGAGGACTGGAGGCTCTCAAGG GCTTCGATAAGGAAAGTGGGCTGTGGGTAATCATGACAACTGAGGTGCCTGAAGCTTGCCAGGAGGCGACTACATCCGGC CGGGCGGGCGATAGTCAAGTTGAGAAGGTGACTCTTCATAGGTTTCTATAGGGGCTGGTCCGGTGCGCTGACACGAGGNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN >R6 NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNTGTATATATAT AAATTTAATATATAATATAAAATATATAACATGTAATAGATGTAATAGGTAATGTTTAATGTGTAATATATAATGTGATA TGTAATATAATATATAATATGCAATATATAAAGAATATGTAACTCTTTAATATCTGTGTGTATATATACATATATACACA CACACACATATGTGTGTGTGTGTGTGTGTGTGTGTCTGTGTGTGTGTGTTCTTTAAAATTTTTGCCAGGCACGATGGTAC ACACCTTTAATCCTAGCACTTGGGAGACAGAGGCATGTGGATCTCTATGAGTTCTAGGCCAGTCAATGCTACATAATGAG TCTTTATCTCAAAGAAACTGTTGGTTTTTTTTTTTTTTAATTTTGTATATGTGTGTGTACCTGTGTGTCTATGCAGCAAC TGACCTGCACCCCGATTTCTCCACTGCTGAGCTGTCTTCCCAGCCCACATTTACCCTTTGGAACGCTGAAGGGGCCGGGA GGGAGGAAGTGTGGGTGAGCAAGGAGGGAGAACTGGAGGCTCTCAGGGGCTTCAGTAAGGAAAGGGTGCTGTGTGTATTC AGGACAACTGAGGTGCCTGAAGCTTGCCAGGAGCCGACTCCAGCCGGCCGGGCGGGCGAGAGTCATGGGAGGAAGTGACT CCTCAGATGTTTCTATAGGGGCTGGCCCGGTGCGCGCACACGAGGGAGTTATCTTTGTTTAATTATTAAATGTGGTTCCT GTTTATGCTCATCTTTCTCACATGGGGGAATCTCGTGGACTCACTGCCGG