FLAM-seq 1.0.0 – Full-length poly(A) and mRNA Sequencing

FLAM-seq 1.0.0

:: DESCRIPTION

FLAM-seq is a rapid and simple method for high-quality sequencing of entire mRNAs.

::DEVELOPER

N. Rajewsky Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

FLAM-seq

:: MORE INFORMATION

Citation

Legnini I, Alles J, Karaiskos N, Ayoub S, Rajewsky N.
FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control.
Nat Methods. 2019 Sep;16(9):879-886. doi: 10.1038/s41592-019-0503-y. Epub 2019 Aug 5. PMID: 31384046.

BioVLAB-MMIA-NGS – miRNA mRNA Integrated Analysis

BioVLAB-MMIA-NGS

:: DESCRIPTION

BioVLAB-MMIA-NGS is a reconfigurable cloud computing environment for microRNA and mRNA integrated analysis using sequencing data

::DEVELOPER

B&H (Bio and Health Informatics) lab , SNU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

BioVLAB-MMIA-NGS

 :: MORE INFORMATION

Citation

BioVLAB-MMIA-NGS: MicroRNA-mRNA Integrated Analysis using High Throughput Sequencing Data.
Chae H, Rhee S, Nephew KP, Kim S.
Bioinformatics. 2014 Sep 29. pii: btu614.

BioVLAB-MMIA: a cloud environment for microRNA and mRNA integrated analysis (MMIA) on Amazon EC2.
Lee H, Yang Y, Chae H, Nam S, Choi D, Tangchaisin P, Herath C, Marru S, Nephew KP, Kim S.
IEEE Trans Nanobioscience. 2012 Sep;11(3):266-72. doi: 10.1109/TNB.2012.2212030.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W356-62. doi: 10.1093/nar/gkp294. Epub 2009 May 6.
MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression.
Nam S1, Li M, Choi K, Balch C, Kim S, Nephew KP.

SNPlice 1.8.0 – Find SNPs influencing splicing in NGS mRNA data

SNPlice 1.8.0

:: DESCRIPTION

SNPlice is a software tool to find and evaluate the co-occurrence of single-nucleotide-polymorphisms (SNP) and altered splicing in next-gen mRNA sequence reads.

::DEVELOPER

The Horvath Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 SNPlice

:: MORE INFORMATION

Citation

SNPlice: Variants that Modulate Intron-retention from RNA-sequencing Data.
Mudvari P, Movassagh M, Kowsari K, Seyfi A, Kokkinaki M, Edwards NJ, Golestaneh N, Horvath A.
Bioinformatics. 2014 Dec 6. pii: btu804

BLAT 36 – Rapid mRNA/DNA & Cross-species Protein Alignments

BLAT 36

:: DESCRIPTION

BLAT (BLAST -like alignment tool) is a bioinformatics software a tool which performs rapid mRNA/DNA and cross-species protein alignments. BLAT is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences.

BLAT Online Version

::DEVELOPER

Jim Kent

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX

:: DOWNLOAD

 BLAT ; Source Code

:: MORE INFORMATION

Citation

Kent, W.J. 2002.
BLAT — The BLAST-Like Alignment Tool.
Genome Research 4: 656-664

MultiMiTar – Predict mRNA Targets of a Given microRNA

MultiMiTar

:: DESCRIPTION

MultiMiTar is an enhancement of TargetMiner with multiobjective feature selection and ranking of the predicted mRNA targets of a given microRNA

::DEVELOPER

Bioinformatics Lab at Machine Intelligence Uni

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MultiMiTar

:: MORE INFORMATION

Citation

Ramkrishna Mitra and Sanghamitra Bandyopadhyay,
MultiMiTar: A Novel Multi Objective Optimization based miRNA-Target Prediction Method“,
PLoS ONE 6(9): e24583. doi:10.1371/journal.pone.0024583.

CisRNA-SVM – Identification of Structured Cis-regulatory Elements in the 3’UTRs of human Protein-coding mRNAs

CisRNA-SVM

:: DESCRIPTION

CisRNA-SVM is a software for genome wide predictions of novel structured RNA cis-regulatory elements in human 3′ UTRs.

::DEVELOPER

Dr Chris Brown’s Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • Perl

:: DOWNLOAD

CisRNA-SVM

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Oct;40(18):8862-73. doi: 10.1093/nar/gks684. Epub 2012 Jul 20.
Computational identification of new structured cis-regulatory elements in the 3′-untranslated region of human protein coding genes.
Chen XS1, Brown CM.

SpliceSeq 2.1 – Investigate alternative mRNA Splicing in Next Generation mRNA Sequence data

SpliceSeq 2.1

:: DESCRIPTION

SpliceSeq provides a quick, easy method of investigating alternative mRNA splicing in next generation mRNA sequence data. The tool may be used on a single mRNA-Seq sample to identify genes with multiple spliceforms or on a pair of samples to identify differential splicing between the samples. Sequence reads are mapped to splice graphs that unambiguously quantify the inclusion level of each exon and splice junction. The graphs are then traversed to predict the protein isoforms that are likely to result from the observed exon and splice junction reads. UniProt annotations are mapped to each protein isoform to identify potential functional impacts of alternative splicing.

::DEVELOPER

Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 SpliceSeq

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Sep 15;28(18):2385-7. Epub 2012 Jul 20.
SpliceSeq: a resource for analysis and visualization of RNA-Seq data on alternative splicing and its functional impacts.
Ryan MC, Cleland J, Kim R, Wong WC, Weinstein JN.

miRtest 1.8 – Combined miRNA- and mRNA-testing

miRtest 1.8

:: DESCRIPTION

Expression levels of mRNAs are among other factors regulated by microRNAs. A particular microRNA can bind specifically to several target mRNAs and lead to their degradation. Expression levels of both, mRNAs and microRNAs, can be obtained by microarray experiments. In order to increase the power of detecting microRNAs that are differentially expressed between two different groups of samples, “miRtest” incorporates expression levels of their related target gene sets.

::DEVELOPER

miRtest team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 miRtest

:: MORE INFORMATION

Citation

PLoS One. 2012;7(6):e38365. doi: 10.1371/journal.pone.0038365. Epub 2012 Jun 19.
Detection of simultaneous group effects in microRNA expression and related target gene sets.
Artmann S1, Jung K, Bleckmann A, Beissbarth T.

PALMA 0.3.7 – mRNA to Genome Alignments using Large Margin Algorithms

PALMA 0.3.7

:: DESCRIPTION

PALMA aligns two genomic sequences in an optimal way according to its underlying algorithm and trained parameters.

::DEVELOPER

the Biomedical Informatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • Python

:: DOWNLOAD

  PALMA

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Aug 1;23(15):1892-900. Epub 2007 May 30.
PALMA: mRNA to genome alignments using large margin algorithms.
Schulze U, Hepp B, Ong CS, Rätsch G.

rNA 1.0 / mrNA 1.0 / grNA 0.9 – randomized Numerical Aligner

rNA 1.0 / mrNA 1.0 / grNA 0.9

:: DESCRIPTION

rNA (randomized Numerical Aligner) is a software able to align the huge amount of data produced by Next Generation Sequencers. The main feature of rNA is the fact that it achieves an accuracy greater than the majority of other tools in a feasible amount of time. rNA works with single as well as paired ends reads and it allows indels and delta-search for better accuracy.

mrNA is the MPI version of the original rNA program.

grNA is a graphical front-end for rNA

::DEVELOPER

bioinformatics team at Istituto di Genomica Applicata (Applied Genomics Institute) andDepartment of Mathematics and Informatics, University of Udine.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • C++ Compiler

:: DOWNLOAD

  rNA / mrNA / grNA

:: MORE INFORMATION

Citation

rNA: a Fast and Accurate Short Reads Numerical Aligner
Vezzi F., Del Fabbro C., Tomescu A.I., and Policriti A.
Bioinformatics, 2011, doi:10.1093/bioinformatics/btr617

mrNA: the MPI randomized Numerical Aligner
Del Fabbro C., Vezzi F., and Policriti A.
Proceedings of 2011 IEEE International Conference on Bioinformatics and Biomedicine (BIBM 2011), Atlanta (Georgia), November 12-15, 2011, IEEE Computer Society 0:139-142, ISBN 978-0-7695-4574-5