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ABSTRACT:
VISualization Tool for Alignments is
a program to depict long sequence alignments of DNA from two
or more organisms with various types of annotation in a clear
and easily interpretable format. Originally it was developed
to locate conserved sequences in syntenic regions.
Key Features:
- Clean graphical output, allowing for easy identification
of sequence similarities and differences
- Easily configurable, enabling the visualization of alignments
of up to several megabases at different levels of resolution
- Displays alignments of draft sequences
- Displays sequence annotations such as repeats, coding
exons, UTRs and more
The VISTA plot is based on moving a user-specified window
over the entire alignment and calculating the percent identity
over the window at each base pair.
AVID is an alignment program designed to work seamlessly
with VISTA. AVID globally aligns DNA sequences of arbitrary
length for the purpose of annotation and biological discovery
using syntenic genomic sequences from two organisms.
Key Features:
- Aligns hundreds of kilobases quickly
- Highly accurate and able to detect weak homologies
- Able to handle one sequence in draft by ordering and orienting
the contigs automatically
- Fast alignment of similar sequences is useful for alignments
of primate sequences or comparison of assemblie
AVID works by recursively finding strong anchors from the
collection of maximal matches in the sequences.
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