jEcho 1.0C – An Evolved Weight Vector to CHaracterize the protein’s post-translational Modification mOtifs

jEcho 1.0C

:: DESCRIPTION

jEcho is an Evolved weight vector to CHaracterize the protein’s posttranslational modification mOtifs.

::DEVELOPER

Health Informatics Lab (HILab)

:: SCREENSHOTS

jEcho

:: REQUIREMENTS

  • Linux/ MacOsX/ Windows
  • Java

:: DOWNLOAD

 jEcho

:: MORE INFORMATION

Citation

Interdiscip Sci. 2015 Jun;7(2):194-9. doi: 10.1007/s12539-015-0260-2. Epub 2015 Aug 6.
jEcho: an Evolved weight vector to CHaracterize the protein’s posttranslational modification mOtifs.
Zhao M, Zhang Z, Mai G, Luo Y, Zhou F.

iRNA-PseColl – Identifying Occurrence Sites of different RNA Modifications

iRNA-PseColl

:: DESCRIPTION

iRNA-PseColl is seamless platform for identifying the occurrence sites of different RNA modifications by incorporating collective effects of nucleotides into PseKNC

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iRNA-PseColl: Identifying the Occurrence Sites of Different RNA Modifications by Incorporating Collective Effects of Nucleotides into PseKNC.
Feng P, Ding H, Yang H, Chen W, Lin H, Chou KC.
Mol Ther Nucleic Acids. 2017 Jun 16;7:155-163. doi: 10.1016/j.omtn.2017.03.006.

iRNA-3typeA – Identifying 3-types of Modification at RNA’s Adenosine Sites

iRNA-3typeA

:: DESCRIPTION

iRNA-3typeA web-server allows for simultaneously identifying the most frequently observed N1-methyladenosine (m1A), N6-methyladenosine (m6A) and adenosine to inosine (A-to-I) modifications in both H. sapiens and M. musculus transcriptomes.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iRNA-3typeA: Identifying Three Types of Modification at RNA’s Adenosine Sites.
Chen W, Feng P, Yang H, Ding H, Lin H, Chou KC.
Mol Ther Nucleic Acids. 2018 Jun 1;11:468-474. doi: 10.1016/j.omtn.2018.03.012.

tRNAmod – Prediciton of tRNA Modifications

tRNAmod

:: DESCRIPTION

The tRNAmod is a web-server for the prediction of transfer RNA (tRNA) modifications. Post-transcriptional modifications of tRNA plays a major role in their functionality. It provides both flexibility as well as rigidity and fine tune tRNA structure for the maximum performance.

::DEVELOPER

tRNAmod team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Prediction of uridine modifications in tRNA sequences.
Panwar B, Raghava GP.
BMC Bioinformatics. 2014 Oct 2;15:326. doi: 10.1186/1471-2105-15-326.

tRNAmodpred – Predicting Posttranscriptional Modifications in tRNAs

tRNAmodpred

:: DESCRIPTION

tRNAmodpred is a method for predicting modifications in tRNA using the MODOMICS database of RNA modification pathways as a reference.

::DEVELOPER

Bujnicki lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 tRNAmodpred

:: MORE INFORMATION

Citation:

tRNAmodpred: a computational method for predicting posttranscriptional modifications in tRNAs.
Machnicka MA, Dunin-Horkawicz S, de Crécy-Lagard V, Bujnicki JM.
Methods. 2016 Mar 22. pii: S1046-2023(16)30047-0. doi: 10.1016/j.ymeth.2016.03.013.

dCMA – differential Chromatin Modification Analysis

dCMA

:: DESCRIPTION

dCMA is a package for identifying cell-type specific genomic regions with distinctive chromatin modifications.

::DEVELOPER

Shihua Zhang’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • MatLab

:: DOWNLOAD

 dCMA

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Nov;41(20):9230-42. doi: 10.1093/nar/gkt712. Epub 2013 Aug 14.
Discovery of cell-type specific regulatory elements in the human genome using differential chromatin modification analysis.
Chen C1, Zhang S, Zhang XS.

miRMOD 0.3 – miRNA Modification Identification tool

miRMOD 0.3

:: DESCRIPTION

miRMOD is the first windows based standalone GUI tool to identify and analyze non templated nucleotide additions and trimming at both the termini of the miRNA sequences in NGS data.

::DEVELOPER

Bioinformatics Centre ICGEB New Delhi

:: SCREENSHOTS

miRMOD

:: REQUIREMENTS

:: DOWNLOAD

 miRMOD

:: MORE INFORMATION

Citation

miRMOD: a tool for identification and analysis of 5′ and 3′ miRNA modifications in Next Generation Sequencing small RNA data.
Kaushik A, Saraf S, Mukherjee SK, Gupta D.
PeerJ. 2015 Oct 20;3:e1332.

histoneHMM 1.4 – Differential Analysis of Histone Modifications with broad Genomic Footprints

histoneHMM 1.4

:: DESCRIPTION

histoneHMM is a software to analyse ChIP-seq data of histone modifications with broad genomic footprints like H3K27me3. It allows for calling modified regions in single samples as well as for calling differentially modified regions in a comparison of two samples.

::DEVELOPER

histoneHMM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 histoneHMM

:: MORE INFORMATION

Citation:

histoneHMM: Differential analysis of histone modifications with broad genomic footprints.
Heinig M, Colomé-Tatché M, Taudt A, Rintisch C, Schafer S, Pravenec M, Hubner N, Vingron M, Johannes F.
BMC Bioinformatics. 2015 Feb 22;16(1):60. doi: 10.1186/s12859-015-0491-6.

HMCan 1.11 – Histone Modification in Cancer

HMCan 1.11

:: DESCRIPTION

HMCan is Hidden Markov Model based tool that is developed to detect histone modification in cancer ChIP-seq data. It applies three correction steps to the data: copy number correction, GC bias correction and noise level correction.

::DEVELOPER

HMCan team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HMCan

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Dec 1;29(23):2979-86. doi: 10.1093/bioinformatics/btt524. Epub 2013 Sep 9.
HMCan: a method for detecting chromatin modifications in cancer samples using ChIP-seq data.
Ashoor H1, Hérault A, Kamoun A, Radvanyi F, Bajic VB, Barillot E, Boeva V.

pyrupred – Prediction of Pyruvoyl Serine Modification

pyrupred

:: DESCRIPTION

pyrupred is a software for the computational predictions of such modified serine sites with Feature Selection based on a Random Forest. Several types of features were considered in our method including PSSM conservation scores, disorders, secondary structures, solvent accessibilities, amino acid factors and amino acid occurrence frequencies.

::DEVELOPER

pyrupred team

:: SCREENSHOTS

pyrupred

:: REQUIREMENTS

  • Windows
  • Java

:: DOWNLOAD

 pyrupred

:: MORE INFORMATION

Citation

PLoS One. 2013 Jun 21;8(6):e66678. Print 2013.
Prediction and Analysis of Post-Translational Pyruvoyl Residue Modification Sites from Internal Serines in Proteins.
Jiang Y1, Li BQ, Zhang Y, Feng YM, Gao YF, Zhang N, Cai YD.