Alview protocols

View
description
Alview computational protocol

Alview specifications

Information


Unique identifier OMICS_10692
Name Alview
Alternative name Alignment Viewer
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data.
Output data Outputs are visualizations of these aligned short reads.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


Add your version

Documentation


Maintainer


  • person_outline Richard Finney <>

Information


Unique identifier OMICS_10692
Name Alview
Alternative name Alignment Viewer
Interface Web user interface
Restrictions to use None
Input data Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data.
Output data Outputs are visualizations of these aligned short reads.
Programming languages C
Computer skills Basic
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Richard Finney <>

Publication for Alignment Viewer

Alview IN pipelines

 (5)
2016
PMCID: 5084120
PMID: 27843753
DOI: 10.1186/s40064-016-3312-0

[…] can be used to further filter the sequences, as required. if only full-length sequences are required, sub-genomic sequences can be selected and deleted from the alignments using a multiple sequence alignment viewer/editor, such as mega6 (tamura et al. 2013), genedoc (nicholas et al. 1997) or aliview (larsson 2014). full-length sequences, or sub-genomic sequences covering a region of interest, […]

2012
PMCID: 3308154
PMID: 22434832
DOI: 10.1093/database/bar064

[…] such as during annotation workshops. (ii) gbrowse (15) (http://gmod.org/wiki/gbrowse), which provides visualization of tracks of annotations completed and in progress; (iii) mauve, a multiple genome alignment viewer (16, 17), and (iv) race-p (http://pir.georgetown.edu/pirwww/race_p/race_p_skate.shtml), which provides an interface for protein curation, including protein name, go functional […]

2010
PMCID: 2884020
PMID: 20552020
DOI: 10.1371/journal.pone.0011087

[…] were obtained from ncbi. plasmid alignments were conducted using progressive alignment option of mauve 2.3.1 [29] with the default settings. figures 7 and 8 were generated using the mauve alignment viewer, which illustrates locally collinear blocks (lcbs) as regions without rearrangements in the homologous backbone sequence. lcbs below a plasmid's center line represent the reverse […]

2007
PMCID: 2031907
PMID: 17850653
DOI: 10.1186/1471-2105-8-333

[…] genome browsers like ensembl ([4]), wormbase [8], and gbrowse [9]. several protein sequence das clients are available like dasty [10], proview [11] or the cbs das viewer [12]. the multiple sequence alignment viewer jalview has recently been extended to support accessing features through das [13]. cargo is a flexible system for visualization and analysis of biological information which among […]

2006
PMCID: 1569441
PMID: 16930487
DOI: 10.1186/1741-7007-4-29

[…] at the periplasm-membrane interface (data not shown)., we aligned all detected pep-cterm domains according to tigr02595 and grouped related sequences by constructing a neighbor-joining tree in the alignment viewer belvu according to their scoredist sequence distances [31]. inspection of the tree (data not shown) shows a clade of 9 pep-cterm domains from colwellia psychreythraea 34h […]

Alview institution(s)
Computational Genomics Research Group, Center for Bioinformatics and Information Technology, National Cancer Institute, Bethesda, MD, USA
Alview funding source(s)
This study is supported by the NCI of the U.S. National Institutes of Health.

Alview reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review Alview