FSFinder 2.0 – Predict Frameshifting in Genomic Sequences

FSFinder 2.0

:: DESCRIPTION

FSFinder (Frameshift Signal Finder) is a software that searches the genomic sequences or mRNA sequences for frameshifting sites.FSFinder is capable of finding -1 frameshift sites for most known genes and +1 frameshift sites for two genes: protein chain release factor (prfB ) and ornithine decarboxylase antizyme (oaz ).

::DEVELOPER

Biocomputing Lab. School of Computer Science and Engineering Inha University, Inchon

:: SCREENSHOTS

:: REQUIREMENTS

Windows
Microsoft .NET Framework

:: DOWNLOAD

FSFinder

:: MORE INFORMATION

Citation

Byun Y, Moon S, Han K.
A general computational model for predicting ribosomal frameshifts in genome sequences.
Comput Biol Med. 2007 Dec;37(12):1796-801. Epub 2007 Aug 2.

Trnascan-SE 2.0.8 – Search for tRNA Genes in Genomic Sequence

Trnascan-SE 2.0.8

:: DESCRIPTION

tRNAscan-SE is a program for improved detection of transfer RNA genes in genomic sequence.

::DEVELOPER

the Lowe Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Trnascan-SE

:: MORE INFORMATION

Citation:

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes.
Lowe TM, Chan PP.
Nucleic Acids Res. 2016 May 12. pii: gkw413.

Lowe, T.M. and Eddy, S.R. (1997)
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.
Nucleic Acids Research, 25, 955-964.

CLARK 1.2.6.1 – Fast and Accurate Classification of Metagenomic and Genomic Sequences

CLARK 1.2.6.1

:: DESCRIPTION

Clark is a novel approach to classify metagenomic reads at the species or genus level with high accuracy and high speed.

::DEVELOPER

Algorithms and Computational Biology Lab ,University of California

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CLARK

:: MORE INFORMATION

Citation

Ounit R, Wanamaker S, Close TJ, Lonardi S,
CLARK: fast and accurate classification of metagenomic and genomic sequences using discriminative k-mers
BMC Genomics 2015, 16:236.

ATRHunter / ATRHunterPlus – Find Approximate Tandem Repeats in a Genomic Sequence

ATRHunter / ATRHunterPlus

:: DESCRIPTION

ATRHUNTER finds and displays approximate tandem repeats (ATR) in DNA sequences. An approximate tandem repeat (ATR) in a genomic sequence is a string of nucleotides repeated consecutively at least twice with some small differences between the repeated copies

ATRHunter Online Version

::DEVELOPER

Laboratory of Computational Biology , Technion

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/ Linux / Mac OsX

:: DOWNLOAD

ATRHUNTER

:: MORE INFORMATION

Citation

Wexler Y, Yakhini Z, Kashi Y, Geiger D.
Finding Approximate Tandem Repeats in Genomic Sequences”
J Comput Biol. 2005 Sep;12(7):928-42

MOST+ 1.5 – Motif Finding system combing Genomic Sequence and Heterogenous Genome-wide Signatures

MOST+ 1.5

:: DESCRIPTION

MOST+ is a fast MOTIF finding tool(MOtif finding by Suffix tree and heterogeneous Tags). It extracts distribution features of nearby epigenomic markers, like histone modification or nucleosome occupancy, to help de novo find motif, thus rendering a higher level of accuracy on characterizing motif (cross-validated by ChIP-seq data) and more co-factors.

::DEVELOPER

Dr. Chaochun Wei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

MOST+

:: MORE INFORMATION

Citation

BMC Genomics. 2015;16 Suppl 7:S13. doi: 10.1186/1471-2164-16-S7-S13.
MOST+: A de novo motif finding approach combining genomic sequence and heterogeneous genome-wide signatures.
Zhang Y, He Y, Zheng G, Wei C.

GenomeScan 1.0 – Prediction of Gene Structures in Genomic Sequences

GenomeScan 1.0

:: DESCRIPTION

GenomeScan is a program for identifying the exon-intron structures of genes in genomic DNA sequences from a variety of organisms, with a focus on human and other vertebrates. The algorithm combines two principal sources of information: 1) models of exon-intron and splice signal composition; and 2) sequence similarity information such as BLASTX hits.

::DEVELOPER

Christopher Burge Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Yeh, R.-F., Lim, L. P., and Burge, C. B. (2001)
Computational inference of homologous gene structures in the human genome.
Genome Res. 11: 803-816.

SPALN 2.3.3f – Mapping and Alignment of a set of cDNA Sequences onto a Genomic Sequence

SPALN 2.3.3f

:: DESCRIPTION

Spaln (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job. Spaln adopts multi-phase heuristics that makes it possible to perform the job on a conventional personal computer running under Unix/Linux with limited memory. The program is written in C++ and distributed as source codes and also as executables for a few platforms. Unless binaries are not provided, users must compile the program on their own system. Although the program has been tested only on a Linux operating system, it is likely to be portable to most Unix systems with little or no modifications. The accessory program sortgrcd sorts the gene loci found by spaln in the order of chromosomal position and orientation.

::DEVELOPER

Computational Biology Research Center (CBRC),

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ compiler

:: DOWNLOAD

SPALN

:: MORE INFORMATION

Citation

Gotoh, O.
“A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence”
Nucleic Acids Research 36 (8) 2630-2638 (2008).

WIsH 1.0 – Prediction of Prokaryotic Hosts of Phages from Genomic Sequences

WIsH 1.0

:: DESCRIPTION

WIsH(Who Is the Host) can identify bacterial hosts from metagenomic data, keeping good accuracy even on smaller contigs.

::DEVELOPER

Söding Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOs
C Compiler

:: DOWNLOAD

WIsH

:: MORE INFORMATION

Citation:

WIsH: who is the host? Predicting prokaryotic hosts from metagenomic phage contigs.
Galiez C, Siebert M, Enault F, Vincent J, Söding J.
Bioinformatics. 2017 Oct 1;33(19):3113-3114. doi: 10.1093/bioinformatics/btx383.

BRANCH 1.8.1 – boosting RNA-Seq Assemblies with Partial or related Genomic Sequences

BRANCH 1.8.1

:: DESCRIPTION

BRANCH is a software that extends de novo transfrags and identifies novel transfrags with DNA contigs or genes of close related species. BRANCH discovers novel exons first and then extends/joins fragmented de novo transfrags, so that the resulted transfrags are more complete.

::DEVELOPER

Girke Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

Linux
LEMON
BLAT

:: DOWNLOAD

BRANCH

:: MORE INFORMATION

Citation

BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences
Ergude Bao, Tao Jiang and Thomas Girke (2013)
Bioinformatics (2013) 29 (10): 1250-1259.doi: 10.1093/bioinformatics/btt127

PPCMatrix 1.25 – Dotmatrix program to Compare large Genomic Sequences against Protein Sequences

PPCMatrix 1.25

:: DESCRIPTION

PPCMatrix is a versatile dotmatrix program for the Apple Macintosh, optimized for the PowerPC.

::DEVELOPER

Bürglin Lab

:: SCREENSHOTS

:: REQUIREMENTS

Apple Macintosh

:: DOWNLOAD

PPCMatrix

:: MORE INFORMATION

CitationThomas R. Bürglin (1998)
PPCMatrix: a PowerPC dotmatrix program to compare large genomic sequences against protein sequences.
Bioinformatics 14: 751-752.