Module Detail Information

Name:Stretcher
Type: Module
Short URL:
http://bit.ly/1B7Eg49
Description:stretcher calculates a global alignment of two sequences using a modification of the classic dynamic programming algorithm which uses linear space. A global pairwise alignment is one where it is assumed that the two sequences have diverged from a common ancestor and that the program should try to stretch the two sequences, introducing gaps where necessary, in order to show the alignment over the whole length of the two sequences that best illustrates their similarities. In contrast, a local alignment program like matcher simply finds local, small parts of the two sequences where there is some similarity and makes no assumption about the whole length of the sequence needing to be similar. The standard sequence global alignment program using the Needleman & Wunsch algorithm, as implemented in the program needle, requires O(MN) space and O(N) time. This is standard computer-science language for it needing an amount of computer memory that is proportional to the product of the two sequences being aligned and taking an amount of time that is proportional to the shorter of the two sequences. So if a 1 kb and a 10 kb sequence take 10 Mega-words of memory and 10 minutes to align, you should expect that in order to align a 10 kb sequence and a 1 Mb sequence you will need appoximately 10 Giga-words of memory and 100 minutes. Computer memory will rapidly be exhausted as the size of the aligned sequences increases. This program implements the Myers and Miller algorithm for finding an optimal global alignment in an amount of computer memory that is only proportional to the size of the smaller sequence - O(N). In computing, a benefit is seldom gained without a cost elsewhere. The cost of gaining a memory-efficient alignment is that it takes about twice the amount of time to do the alignment as the Needleman & Wunsch algorithm. In computer-science language the time is approximately O(2N).
Executable:
/stretcher
Input Parameters:
 - A Sequence
 - B Sequence
 - A Start
 - A End
 - A Reverse
 - A Ask
 - A Nucleotide
 - A Protein
 - A Lower Case
 - A Upper Case
 - A Format
 - A Database Name
 - A Entry Name
 - A UFO Features
 - A Features Format
 - A Features File
 - Gap Opening Penalty
 - Gap Extension Penalty
 - B Start
 - B End
 - B Reverse
 - B Ask
 - B Nucleotide
 - B Protein
 - B Lower Case
 - B Upper Case
 - B Format
 - B Database Name
 - B Entry Name
 - B UFO Features
 - B Features Format
 - B Features File
 - Alignment format
 - File Name extension
 - Output directory
 - Base file name
 - Alignment width
 - Show Accession Number
 - Show Description
 - Show Full USA
 - Show Full sequence
 - Turn Off Prompts
 - Standard Output
 - Filter
 - Options
 - Debug
 - Verbose
 - Help
 - Report Warnings
 - Report Errors
 - Report Fatal Errors
 - Report Dying Program Messages
 - Scoring Matrix File
Output Parameters:
 - Output
File size:36.04 KB
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