+357 22392624, + 357 22392852
level 2 topic image

Analysis tools

Protein analysis tools

Standalone tools

1)      http://hmmer.org/-HMMER - biosequence analysis using profile hidden Markov models

 

Web applications and data repositories

1)      CATH-Gene3D database describes protein families and domain architectures in complete genomes. Protein families are formed using a Markov clustering algorithm, followed by multi-linkage clustering according to sequence identity. Mapping of predicted structure and sequence domains is undertaken using hidden Markov models libraries representing CATH and Pfam domains. CATH-Gene3D is based at University College, London, UK.

2)      CDD is a protein annotation resource that consists of a collection of annotated multiple sequence alignment models for ancient domains and full-length proteins. These are available as position-specific score matrices (PSSMs) for fast identification of conserved domains in protein sequences via RPS-BLAST. CDD content includes NCBI-curated domain models, which use 3D-structure information to explicitly define domain boundaries and provide insights into sequence/structure/function relationships, as well as domain models imported from a number of external source databases.

3)      HAMAP stands for High-quality Automated and Manual Annotation of Proteins. HAMAP profiles are manually created by expert curators. They identify proteins that are part of well-conserved proteins families or subfamilies. HAMAP is based at the SIB Swiss Institute of Bioinformatics, Geneva, Switzerland.

4)      PANTHER is a large collection of protein families that have been subdivided into functionally related subfamilies, using human expertise. These subfamilies model the divergence of specific functions within protein families, allowing more accurate association with function, as well as inference of amino acids important for functional specificity. Hidden Markov models (HMMs) are built for each family and subfamily for classifying additional protein sequences. PANTHER is based at at University of Southern California, CA, US.

5)      Pfam is a large collection of multiple sequence alignments and hidden Markov models covering many common protein domains. Pfam is based at EMBL-EBI, Hinxton, UK.

6)     PIRSF protein classification system is a network with multiple levels of sequence diversity from superfamilies to subfamilies that reflects the evolutionary relationship of full-length proteins and domains. PIRSF is based at the Protein Information Resource, Georgetown University Medical Centre, Washington DC, US.

7)      PRINTS is a compendium of protein fingerprints. A fingerprint is a group of conserved motifs used to characterise a protein family or domain. PRINTS is based at the University of Manchester, UK.

8)      ProDom protein domain database consists of an automatic compilation of homologous domains. Current versions of ProDom are built using a novel procedure based on recursive PSI-BLAST searches. ProDom is based at PRABI Villeurbanne, France.

9)      PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family a new sequence belongs. PROSITE is base at the Swiss Institute of Bioinformatics (SIB), Geneva, Switzerland.

10)   SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures. SMART is based at at EMBL, Heidelberg, Germany.

11)   SUPERFAMILY is a library of profile hidden Markov models that represent all proteins of known structure. The library is based on the SCOP classification of proteins: each model corresponds to a SCOP domain and aims to represent the entire SCOP superfamily that the domain belongs to. SUPERFAMILY is based at the University of Bristol, UK.

12)   TIGRFAMs is a collection of protein families, featuring curated multiple sequence alignments, hidden Markov models (HMMs) and annotation, which provides a tool for identifying functionally related proteins based on sequence homology. TIGRFAMs is based at the J. Craig Venter Institute, Rockville, MD, US.

13)    https://www.ebi.ac.uk/interpro/search/sequence-searchInterproScan -  provides functional analysis of proteins by classifying them into families and predicting domains and important sites. Combines protein signatures from a number all of the above member databases into a single searchable resource

 

 

RNA sequence analysis tools

https://www.tbi.univie.ac.at/RNA/-The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures

MicroRNAs – databases and tools for target prediction

miRDB

tool - target prediction

http://www.mirdb.org

microRNA.org

tool - target prediction

http://microrna.org

PicTar

tool - target prediction

http://pictar.mdc-berlin.de

TargetScan

tool - target prediction

http://www.targetscan.org

RNA22

tool - target prediction

http://cm.jefferson.edu/rna22v1.0-homo_sapiens

TargetProfiler

tool - target prediction

http://mirna.imbb.forth.gr/Targetprofiler.html

DIANA-microT-CDS

tool - target prediction

http://www.microrna.gr/microT-CDS

TargetMiner

tool - target prediction

http://www.isical.ac.in/~bioinfo_miu/targetminer20.htm

PITA

tool - target prediction

http://genie.weizmann.ac.il/pubs/mir07/

GeneTrail

tool - gene set analysis

http://genetrail.bioinf.uni-sb.de

miRGator

tool - Integrated system for functional investigation of miRNAs

http://mirgator.kobic.re.kr

miTalos

tool - prediction and visualization of miRNA signaling pathways

http://mips.helmholtz-muenchen.de/mitalos

DIANA-miRPath

tool - prediction and visualization of miRNA pathways

http://www.microrna.gr/miRPathv2

wapRNA

tool - RNA-Seq data analysis

http://waprna.big.ac.cn

DSAP

tool - RNA-Seq data analysis

http://dsap.cgu.edu.tw

miRanalyzer

tool - RNA-Seq data analysis

http://bioinfo2.ugr.es/miRanalyzer/miRanalyzer.php

miRCat

tool - RNA-Seq data analysis

http://srna-tools.cmp.uea.ac.uk/animal/cgi-bin/srna-tools.cgi?rm=input_form&tool=mircat

mirTools

tool - RNA-Seq data analysis

http://122.228.158.106/mr2_dev/

miRBase

database - miRNA repository

http://www.mirbase.org

S-MED/CC-MED

database - miRNA expression data

http://www.oncomir.umn.edu/SMED & http://www.oncomir.umn.edu/colon/basic_search.php

smirnaDB

database - miRNA expression data

http://www.mirz.unibas.ch/cloningprofiles

miRNEYE

database - miRNA expression data

http://mirneye.tigem.it

microRNA.org — miRNA Expression

database - miRNA expression data

http://www.microrna.org/microrna/getExprForm.do

miRTarBase

database - of  manually curated mirna targets

http://mirtarbase.mbc.nctu.edu.tw

DIANA-TarBase

database - of  manually curated mirna targets

http://www.microrna.gr/tarbase

miRecords

database - of  manually curated mirna targets

http://mirecords.biolead.org

 

 

 

miRSel

database/tool - text mined and manually curated targets

http://services.bio.ifi.lmu.de/mirsel/

StarBase

database - of sequence related miRNA experiments

http://starbase.sysu.edu.cn

PhenomiR

database - miRNA associated phenotypes

http://mips.helmholtz-muenchen.de/phenomir

miR2Disease

database - miRNA associated diseases

http://www.mir2disease.org

HMDD

database - miRNA associated diseases

http://202.38.126.151/hmdd/mirna/md

miRenvironment

database - validated miRNA environmental associations

http://202.38.126.151/hmdd/tools/miren.html

Patrocles

database – of polymorphic miRNA-target interactions

http://www.patrocles.org/

 

 

Data Management, Pipeline, Viewing and Repository Systems

1) http://genome.ucsc.edu/index.htmlUSCS Genome Browser

2) https://usegalaxy.org/Galaxy