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General Category >> Help and How-to >> frequency matrix for generic sequences from file https://forum.ugene.net/forum/YaBB.pl?num=1348314040 Message started by karen on Sep 22^{nd}, 2012 at 6:40pm |
Title: frequency matrix for generic sequences from file Post by karen on Sep 22^{nd}, 2012 at 6:40pm
Good morning,
I've just discovered UGENE and found in the documentation that a frequency matrix can be created from a file: "To create a position weight or frequency matrix from an alignment or a file with several sequences, press the Build new matrix button in the Weight matrix search dialog, or select the Tools ‣ Weight matrix ‣ Build weight matrix program main menu item" Below I pasted a FASTA representation, could the frequency matrix be created for it in UGENE? Thanks so much for any hint. Karen >1001 CCCACCACCCCCACCACACCACACCACCCCAAA >1003 CTCCTTCACTTTCAATTAACAAACAACCAAAATCCATAAAAACCCAAAAACTATACCTAATAATATTCTCCCT >1005 CCCCTCTTCCCTTCCT >1012 AACCAAACCAAACAAAATCAAACTAATAATAAAAATCAAAACATAACAAAAAACCCTCCCCAAACCAAATCATAATCCAAAACCAACCTAAATCCTATTCCATCCACACAAACCCAAACTCAAA >1017 CACAACACAATCAAACCAAAACAACCATCCCTCTCCATAACCAACAAACAACCAACCACCAACACAACCAAAACAAAACCACAAAAAACCAAACACAACCAAAACCACAACAACAAATCCT >1022 CACCCACAACCCCACAACACAAACAACACACCCCACAA >1024 AAAAAAAAACCCCAAAAACAAAAAACACCACCATCACTAATCCATCTCATACCAACCC >1026 AAAAAAAAAACACAATCCTCCAACACAACCCACAACACAACAAAAAAACAACAAATCAATAAAAAATTTCTTCCCAAAAATTTCTAAAATCTATTTTCTTTTCTTACAAA >1027 ATAATAACACAAAAAAAAAAAAAAACCACAAACAAAAAAACTTATTCATAATATTCCCCAAA >1029 CCCCATCTCCCCCTCCCCCATCCCTCTCACTCCCCCCCTTTCCCTTTAAAAA >1030 AAAAAATCCCCTTCCCCTTCCCCTTTCCTAATTATTCCCCCCCCCCCTTTTTCCCTCTTCTACACCAAATATCCCTTAAAAATCCCCTCCAAACCTTTAACCCACCACAATTCTTTATTAT >1033 CACACACCAAAAAATCACTATACC >1035 AAAAAAACAAACCAAAAACAC >1037 CTCCTACACACCCCTCCTT >1044 CCCCACAACCTCCAATCACAACCCCCC >1052 ATCCCACATCTACTTCATACACATACAAA >1053 CCAACTCCCTCCCTCTCCTACCCCC >1055 AAAAAAAAAAACCTAAACCAACAAAACCAAAAACTACAACACTACCAATTTCCTTTAAATTAAACCTTACC >1057 CACACAACAAAACACTCCAAAACTCCACCTAACACCCAATCCACACACCCAAACACAAACAAAAATAAAAAAAAAACACCAAAAAACCACAACAATCCCCAAA >1067 CCCCAAACCCAAAAAAACCCCAAAACCCCCCCCCCCCCCTTCCTCTTATTATCCACTACCCCCAAAAATTAAATTAAAATTAATTAATATATAATCTATATTTCTTTTCCCACATTCTTTTCCCCACAAA >1068 CACCACAACCACCACCACCCCCCACTTCATATATCAATATACAACCAACATCCTCCCTCAAACTAATCCAAAACCTCCCCCCAAAAA >1073 CCAAAAAACAAATCAAAAATCCAATAATTCCACTTTTTAAATTACCTTCTCTATATATAACTCAAACAACA >1088 CCCACAATCACCTCCTCCTTCTCCCTAATATACACCCCCACACCACACATCCAATCAATCATCTTTTTTTCCAAAATTTTTCCCCCAAACTAAAAACATATCCCCATACCCCCCCCCCCCCCTTATTATTTTAA >1114 ACTCACACAAAATTCCCAATCTAAAATCACATTCACTATTCACTTTCTAATATTTCCTTAAAATACATAAAACCAAAAATCCTATTTTCACTACACAC >1122 CAAAAACCCCAAAAACCTTTCCTTTCTTCCCCTTTAAAATAAACTCCATCAACCCTAAATAAAAATCCTCCCAAACAAAAAA >1145 TTTCCTCTTTTTTTTTTTTTTCTCCTTTTTTTTTATTATTTATTATATATCTTAACATTTAATAATTACTTAATTTTATATTCTCTCCTTTTTTTTTTCTCTTTTTTTTAAATTTCCTAATTTTAATTATTTCACAATTCTAATTTCCACATTTATAG >1146 CCCTACTCATACTCTCCACTACCCAACACTCCTTCAATTAAATTTAATTCATTACCTTATACTACCATTAACACCCAAAAAATTTCTCACTTTTATTTTTAATTTTTCTATCAAATTAAATCCATCCATTA >1157 CTCTAATTTTCATCCATTTCCCACCTTTACAACAAAACCTAAAATAAAATTTCCCAATTCAACTTCCAAACAATCTCTTAATTATCTTCCAATAATACTCATTAAAAAAATTCTCCAACCAACC >1161 ACACTCATATCCAATTTATATCTCCAAAAAACTCATATAATACCCTACATTACTTATTCCCAACCACCTACAACAAAATCTCATCATTTAAA >1164 TCTCCTATCTTCTTATAA >1187 AAAACCACAACAAAAAAACCAAAAAACCCAAAAACTCCCCTTCTCCTTCTCTCAATAAATCATAATTCTCCTTTTCTCCTTTCTTCTTTTTTTTTATACCATAAATATACCTAATAA >1196 CTCCACACACTCTACAAATCATCAACTATCCCCCAACACTCTCCCTTCCCCTTCCCCCCCCTAAACTAATCCCAAAAAAAAACCCCACCACAACCCCAAAAAAAAA >1206 CTTCAAACCCCACAAACCTACATATACCTACAAAATTCACCAACAA |
Title: Re: frequency matrix for generic sequences from file Post by Yuriy Vaskin on Sep 24^{th}, 2012 at 4:07pm
Hello Karen,
thank you for using UGENE. Usually a frequency matrix is built over sequences of the same length and without gaps. For instance, in your data, minimum sequence length is 18. So positions of a frequency matrix greater than 18 would not make sense. You can try to cut you alignment using "Edit" context menu of MAlignment view or delete some sequences. By the way, for what do you need the matrix? Maybe there is another way in UGENE to do that. |
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