Team:OUC-R/Software
Background
In order to find out whether App sequence - cross sequence system exists in the body, we designed two software respectively: cross sequence searcher software and App sequence searcher software, to determine whether App sequence and cross sequence exist simultaneously in genes, and determine whether they exist in correlation by the position relationship of the two. In this case, we use JAVASRCIPT to design the relevant program, so that it can run directly in the browser, without relying on the strict compilation environment.
Cross Sequence Searcher
Design
A cross sequence on a double strand corresponds to a palindrome sequence on a single strand. A palindrome sequence is a sequence of the form ABCD(NN)DCBA, of which the length can be changed. This means that the user not only needs to enter the sequence to be tested, but also to specify the stem length separately, so that the computer can begin to recognize all the sequences that match the user's input and store the results accordingly.
For the program, the detected palindrome sequence that meets the requirements will be displayed in the output column with its position relative to the detection sequence.
Results
For example, the user specifies a palindrome sequence of stem length 7 and ring length 3, and provides with the sequence:
ATGAAACTCTACAATCTGAAAGATCACAACGAGCAGGTCAGCTTTGCGCAAGCCGTAACCCAGGGGTTGG
GCAAAAATCAGGGGCTGTTTTTTCCGCACGACCTGCCGGAATTCAGCCTGACTGAAATTGATGAGATGCTG
AAGCTGGATTTTGTCACCCGCAGTGCGAAGATCCTCTCGGCGTTTATTGGTGATGAAATCCCACAGGAAAT
CCTGGAAGAGCGCGTGCGCGCGGCGTTTGCCTTCCCGGCTCCGGTCGCCAATGTTGAAAGCGATGTCGG
TTGTCTGGAATTGTTCCACGGGCCAACGCTGGCATTTAAAGATTTCGGCGGTCGCTTTATGGCACAAATGC
TGACCCATATTGCGGGTGATAAGCCAGTGACCATTCTGACCGCGACCTCCGGTGATACCGGAGCGGCAGT
GGCTCATGCTTTCTACGGTTTACCGAATGTGAAAGTGGTTATCCTCTATCCACGAGGCAAAATCAGTCCACT
GCAAGAAAAACTGTTCTGTACATTGGGCGGCAATATCGAAACTGTTGCCATCGACGGCGATTTCGATGCCT
GTCAGGCGCTGGTGAAGCAGGCGTTTGATGATGAAGAACTGAAAGTGGCGCTAGGGTTAAACTCGGCTA
ACTCGATTAACATCAGCCGTTTGCTGGCGCAGATTTGCTACTACTTTGAAGCTGTTGCGCAGCTGCCGCAG
GAGACGCGCAACCAGCTGGTTGTCTCGGTGCCAAGCGGAAACTTCGGCGATTTGACGGCGGGTCTGCTG
GCGAAGTCACTCGGTCTGCCGGTGAAACGTTTTATTGCTGCGACCAACGTGAACGATACCGTGCCACGTTT
CCTGCACGACGGTCAGTGGTCACCCAAAGCGACTCAGGCGACGTTATCCAACGCGATGGACGTGAGTCAG
CCGAACAACTGGCCGCGTGTGGAAGAGTTGTTCCGCCGCAAAATCTGGCAACTGAAAGAGCTGGGTTATG
CAGCCGTGGATGATGAAACCACGCAACAGACAATGCGTGAGTTAAAAGAACTGGGCTACACTTCGGAGCC
GCACGCTGCCGTAGCTTATCGTGCGCTGCGTGATCAGTTGAATCCAGGCGAATATGGCTTGTTCCTCGGCA
CCGCGCATCCGGCGAAATTTAAAGAGAGCGTGGAAGCGATTCTCGGTGAAACGTTGGATCTGCCAAAAGA
GCTGGCAGAACGTGCTGATTTACCCTTGCTTTCACATAATCTGCCCGCCGATTTTGCTGCGTTGCGTAAATT
GATGATGAATCATCAGTAA
Then, the result would be:
App Sequence Searcher
Design
Although the App sequence is supposed to be a purine-pyrimidine alternating sequence of pairs, according to professor Liang, App is sometimes not arranged strictly according to this rule, so we tend to think that the App sequence allows a set of bases that do not conform to the purine-pyrimidine alternating sequence. We put that into account when designing our software. Our computer program requires the user to specify a length range and input a sequence to be detected, so that the computer will find all the sequences that match the user's input and calibrate their position in the sequence.
It's important to note that we didn't design the software to do anything with App sequences of odd lengths, leaving it up to the user to choose whether to add or remove a base at either end, which turns the length of the sequence even.
Results
For example, the user specifies the app sequence with a length range of 8-12bp and provides the same example sequence, Then, the result would be:
Our software:
Stem Loop Finding
App Finding
