:: DESCRIPTION
LSGSP is the java codes which provided for use on this site are not part of the book Large-Scale Genome Sequence Processing published by Imperial College Press
::DEVELOPER
Masahiro Kasahara & Shinichi Morishita
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
miREval is an online tool that can simultaneously search up to 100 sequences for novel microRNAs (miRNAs) in multiple organisms.
::DEVELOPER
Centenary Institute – Bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Gao D, Middleton R, Rasko JE, Ritchie W.
miREval 2.0: a web tool for simple microRNA prediction in genome sequences.
Bioinformatics. 2013 Dec 15;29(24):3225-6. doi: 10.1093/bioinformatics/btt545. Epub 2013 Sep 18. PMID: 24048357; PMCID: PMC5994938.
:: DESCRIPTION
JolyTree implements an alignment-free distance-based procedure for inferring phylogenetic trees from genome contig sequences. For each pair of genomes, a dissimilarity measure is first computed and next transformed to obtain an estimation of the number of substitution events that have occurred during their evolution.
::DEVELOPER
Alexis Criscuolo (alexis.criscuolo@pasteur.fr)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Alexis Criscuolo,
A fast alignment-free bioinformatics procedure to infer accurate distance-based phylogenetic trees from genome assemblies
Research Ideas and Outcomes, 2019, 5:e36178.
:: DESCRIPTION
ReviSeq is a free tool to generate and to revise a bacterial genome sequence from short sequence reads and a reference sequence.
::DEVELOPER
:: SCREENSHOTS
Command
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Genomics. 2012 Nov;100(5):271-6. doi: 10.1016/j.ygeno.2012.07.015. Epub 2012 Aug 10.
Improved variation calling via an iterative backbone remapping and local assembly method for bacterial genomes.
Tae H, Settlage RE, Shallom S, Bavarva JH, Preston D, Hawkins GN, Adams LG, Garner HR.
:: DESCRIPTION
Phusion is a software package for assembling genome sequences from whole genome shotgun(WGS) reads.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
The phusion assembler.
Mullikin JC and Ning Z
Genome research2003;13;1;81-90
:: DESCRIPTION
Hobbes is a software package for efficiently mapping DNA snippets (reads) against a reference DNA sequence. It can map short and long reads, and supports Hamming distance (only substitutions) and edit distance (substitutions/insertions/deletions). Hobbes accepts both single-end and paired-end reads for alignment, and can run on multiple CPU cores using multithreading.
::DEVELOPER
CBCL Lab (Computational Biology and Computational Learning) @ UCI
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
BMC Bioinformatics. 2014 Feb 5;15:42. doi: 10.1186/1471-2105-15-42.
Improving read mapping using additional prefix grams.
Kim J, Li C, Xie X
Nucleic Acids Res. 2012 Mar;40(6):e41. doi: 10.1093/nar/gkr1246. Epub 2011 Dec 22.
Hobbes: optimized gram-based methods for efficient read alignment.
Ahmadi A, Behm A, Honnalli N, Li C, Weng L, Xie X.
:: DESCRIPTION
perEditor (Personal Genome Editor) changes the reference human genome (NCBI36/hg18) into an individual genome, taking into account single nucleotide polymorphisms (SNPs), insertions and deletions, copy number variation, and chromosomal rearrangements. perEditor outputs two alleles (maternal, paternal) of the individual genome that is ready for mapping ChIP-seq and RNA-seq reads, and enabling the analyses of allele specific binding, chromatin structure, and gene expression.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2011 Dec 15;27(24):3427-9. Epub 2011 Oct 17.
Mapping personal functional data to personal genomes.
Rivas-Astroza M, Xie D, Cao X, Zhong S.
:: DESCRIPTION
Atlas-Link links and orients genome sequence contigs into scaffolds quickly and accurately using mate-pair information. Atlas-Link can also be used to superscaffold existing genome assemblies with data from new sequencing technologies.
::DEVELOPER
Human Genome Sequencing Center, Baylor College of Medicine
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
:: DESCRIPTION
LTR_Finder is an efficient program for finding full-length LTR retrotranspsons in genome sequences.
::DEVELOPER
Theoretical Life Sciences Research Center
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Zhao Xu, Hao Wang,
“LTR_FINDER: an efficient tool for the prediction of full-length LTR retrotransposons“,
Nucleic Acids Res. 2007 July; 35(Web Server issue): W265-W268.
:: DESCRIPTION
GenePalette allows genome sequence visualization and navigation. Users can download from NCBI’s GenBank database large or small segments of genome sequence from a variety of organisms preserving the gene annotation that is associated with that sequence. Sequence elements of interest (transcription factor binding sites, etc. can be searched for and identified in the loaded sequence, and then clearly visualized within a colorful graphical representation of gene organization.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Rebeiz M, Posakony JW.
GenePalette: a universal software tool for genome sequence visualization and analysis.
Dev Biol. 2004 Jul 15;271(2):431-438.