MAVG: locating non-overlapping maximum average segments in a given sequence
نویسندگان
چکیده
SUMMARY MAVG is a software tool for finding k non-overlapping maximum-average segments that are sufficiently long in a given sequence of real numbers, for any k > 0. It has applications in several areas of biomolecular sequence analysis including locating GC-rich regions and CpG islands in a genomic sequence, and annotating multiple sequence alignments. AVAILABILITY http://iubio.bio.indiana.edu/soft/molbio/pattern/cpg_islands/.
منابع مشابه
Definitions and Algorithms in SEGID
Given a (multiple) sequence alignment, SEGID first converts it into a sequence of numbers, where each number is the alignment score of a column. (SEGID also directly accepts a sequence of numbers as input.) Then it provides three algorithms to identify conserved segments (high score substrings): 1. Longest segment (with average value lower bound): given a string of numbers and a number A, find ...
متن کاملEfficient Algorithms for Locating the Length-Constrained Heaviest Segments, with Applications to Biomolecular Sequence Analysis
We study two fundamental problems concerning the search for interesting regions in sequences: (i) given a sequence of real numbers of length n and an upper bound U , find a consecutive subsequence of length at most U with the maximum sum and (ii) given a sequence of real numbers of length n and a lower bound L, find a consecutive subsequence of length at least L with the maximum average. We pre...
متن کاملPeople Re-identification in Non-overlapping Field-of-views using Cumulative Brightness Transform Function and Body Segments in Different Color Spaces
Non-overlapping field-of-view (FOV) cameras are used in surveillance system to cover a wider area. Tracking in such systems is generally performed in two distinct steps. In the first step, people are identified and tracked in the FOV of a single camera. In the second step, re-identification of the people is carried out to track them in the whole area under surveillance. Various conventional fea...
متن کاملOptimal algorithms for locating the longest and shortest segments satisfying a sum or an average constraint
We study several fundamental problems arising from biological sequence analysis. Given a sequence of real numbers, we present two linear-time algorithms, one for locating the “longest” sum-constrained segment, and the other for locating the “shortest” sumconstrained segment. These two algorithms are based on the same framework and run in an online manner, hence they are capable of handling data...
متن کاملNon-zero probability of nearest neighbor searching
Nearest Neighbor (NN) searching is a challenging problem in data management and has been widely studied in data mining, pattern recognition and computational geometry. The goal of NN searching is efficiently reporting the nearest data to a given object as a query. In most of the studies both the data and query are assumed to be precise, however, due to the real applications of NN searching, suc...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Bioinformatics
دوره 19 1 شماره
صفحات -
تاریخ انتشار 2003