alv: a console-based viewer for molecular sequence alignments
نویسندگان
چکیده
منابع مشابه
LALNVIEW: a graphical viewer for pairwise sequence alignments
LALNVIEW is a graphical program for visualising local alignments between two sequences (protein or nucleic acids). Sequences are represented by coloured rectangles to give an overall picture of their similarities. LALNVIEW can display sequence features (exon, intron, active site, domain, propeptide, etc.) along with the alignment. When using LALNVIEW through our Web servers, sequence features a...
متن کاملViewing multiple sequence alignments with the JavaScript Sequence Alignment Viewer (JSAV)
The JavaScript Sequence Alignment Viewer (JSAV) is designed as a simple-to-use JavaScript component for displaying sequence alignments on web pages. The display of sequences is highly configurable with options to allow alternative coloring schemes, sorting of sequences and 'dotifying' repeated amino acids. An option is also available to submit selected sequences to another web site, or to other...
متن کاملCodonLogo: a sequence logo-based viewer for codon patterns
MOTIVATION Conserved patterns across a multiple sequence alignment can be visualized by generating sequence logos. Sequence logos show each column in the alignment as stacks of symbol(s) where the height of a stack is proportional to its informational content, whereas the height of each symbol within the stack is proportional to its frequency in the column. Sequence logos use symbols of either ...
متن کاملEstimation and reliability of molecular sequence alignments.
The problem of estimating the relatedness of a pair of biological sequences is addressed. A stochastic model of sequence evolution is described that allows insertion and deletion as well as replacement of amino acid residues (or substitution of nucleotides) over time. An expectation-maximization (EM) algorithm that obtains maximum likelihood estimates of the model parameters is introduced. The ...
متن کاملA Linear Programming Based Algorithm for Multiple Sequence Alignments
In this brief paper we discuss an approach to multiple sequence alignment based on treating the alignmenet process as a stochastic control problem. The use of a model based on a Markov decision process leads to a linear programming problem whose solution is linked to a suggested alignment. Our goal is to avoid the expense in time and computation encountered when dynamic programming based algori...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
ژورنال
عنوان ژورنال: Journal of Open Source Software
سال: 2018
ISSN: 2475-9066
DOI: 10.21105/joss.00955