BioDownloader 2.2.1.0- Download and/or Update Files from Servers

BioDownloader 2.2.1.0

:: DESCRIPTION

BioDownloader is a program for downloading and/or updating files from ftp/http servers. The program has unique features that are specifically designed to deal with bioinformatics data files and servers (large file sets, selective file retrieval, built-in download settings repository, wizard for post- download file processing, simultaneous download of multiple files). Besides the intuitive BioDownloader’s features that allow the user to use it out-of-the-box, provides the experienced user a vast set of fine-tunning options and advanced features.

::DEVELOPER

Dunbrack Lab

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

BioDownloader

:: MORE INFORMATION

Citation

Maxim V. Shapovalov; Adrian A. Canutescu; Roland L. Dunbrack Jr.
BioDownloader: Bioinformatics downloads and updates in a few clicks.
Bioinformatics 2007; doi: 10.1093/bioinformatics/btm120

SALIGN r205 – Multiple Protein Sequence/Structure Alignment Server

SALIGN r205

:: DESCRIPTION

SALIGN is a general alignment module of the modeling program MODELLER. The alignments are computed using dynamic programming, making use of several features of the protein sequences and structures

::DEVELOPER

Andrej Sali Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Aug 1;28(15):2072-3. doi: 10.1093/bioinformatics/bts302. Epub 2012 May 21.
SALIGN: a web server for alignment of multiple protein sequences and structures.
Braberg H1, Webb BM, Tjioe E, Pieper U, Sali A, Madhusudhan MS.

PANNZER2 – Protein Functional Annotation Server

PANNZER2

:: DESCRIPTION

PANNZER (Protein ANNotation with Z-scoRE) is a fully automated service for functional annotation of prokaryotic and eukaryotic proteins of unknown function. The tool is designed to predict the functional description (DE), EC numbers and GO classes.

::DEVELOPER

Liisa Holm’s Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
MySQL
Blast

:: DOWNLOAD

PANNZER2

:: MORE INFORMATION

Citation

Törönen P, Medlar A, Holm L.
PANNZER2: a rapid functional annotation web server.
Nucleic Acids Res. 2018 Jul 2;46(W1):W84-W88. doi: 10.1093/nar/gky350. PMID: 29741643; PMCID: PMC6031051.

PANNZER: high-throughput functional annotation of uncharacterized proteins in an error-prone environment.
Koskinen P, Törönen P, Nokso-Koivisto J, Holm L.
Bioinformatics. 2015 Jan 8. pii: btu851

RaptorX / RaptorX-SS8 – Protein Structure Prediction Server

RaptorX / RaptorX-SS8

:: DESCRIPTION

RaptorX is a protein structure prediction server developed by Xu group, excelling at predicting 3D structures for protein sequences without close homologs in the Protein Data Bank (PDB). Given an input sequence, RaptorX predicts its secondary and tertiary structures as well as solvent accessibility and disordered regions. RaptorX also assigns the following confidence scores to indicate the quality of a predicted 3D model: P-value for the relative global quality, GDT (global distance test) and uGDT (un-normalized GDT) for the absolute global quality, and RMSD for the absolute local quality of each residue in the model. RaptorX-Binding is a web server that predicts the binding sites of a protein sequence, based upon the predicted 3D model by RaptorX.

RaptorX-SS8 is a software package that predicts both 3-class and 8-class protein secondary structure using a probabilistic graphical model Conditional Neural Fields (CNFs).

::DEVELOPER

Jinbo Xu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

RaptorX , RaptorX-SS8

:: MORE INFORMATION

Citation:

Morten Källberg, Haipeng Wang, Sheng Wang, Jian Peng, Zhiyong Wang, Hui Lu & Jinbo Xu.
Template-based protein structure modeling using the RaptorX web server.
Nature Protocols 7, 1511–1522, 2012.

Proteomics. 2011 Oct;11(19):3786-92. doi: 10.1002/pmic.201100196.
Protein 8-class secondary structure prediction using conditional neural fields.
Wang Z, Zhao F, Peng J, Xu J.

ChIP-Seq 1.5.5 – ChIP-Seq Analysis server

ChIP-Seq 1.5.5

:: DESCRIPTION

The ChIP-Seq Web Server provides access to a set of useful tools performing common ChIP-Seq data analysis tasks, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. Users can analyse their own data by uploading mapped sequence tags in various formats, including BED and BAM. The server also provides access to hundreds of publicly available data sets such as ChIP-seq data, RNA-seq data (i.e. CAGE), DNA-methylation data, sequence annotations (promoters, polyA-sites, etc.), and sequence-derived features (CpG, phastCons scores).

::DEVELOPER

Computational Cancer Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Web Server

:: DOWNLOAD

ChIP-Seq

:: MORE INFORMATION

Microtaxi – Microbial Taxonomic Identification and Classification Server

Microtaxi

:: DESCRIPTION

Microtaxi uses an taxon-specific gene based approach and provides an alternate valuable methodology to carry out the taxonomic classification of newly sequenced or existing bacterial genomes.

::DEVELOPER

MetaBioSys laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl

:: DOWNLOAD

Microtaxi

:: MORE INFORMATION

Citation

BMC Genomics. 2015 May 20;16:396. doi: 10.1186/s12864-015-1542-0.
Using the taxon-specific genes for the taxonomic classification of bacterial genomes.
Gupta A, Sharma VK

EPISOFT – Epitope Vaccine Optimization Server

EPISOFT

:: DESCRIPTION

EPISOFT predicts epitope HLA I binding profiles and computes population protection (PPC). It also identifies minimal sets of epitopes that reach a target PPC for 5 distinct user-selected ethnic groups.

::DEVELOPER

Immunomedicine Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Towards the Knowledge-based Design of Universal Influenza Epitope Ensemble Vaccines.
Sheikh QM, Gatherer D, Reche PA, Flower DR.
Bioinformatics. 2016 Jul 10. pii: btw399.

PDEXK – Server for Detection of new Protein Families from the PD-(D/E)XK Superfamily

PDEXK

:: DESCRIPTION

The PDEXK server is developed for detecting new protein families of the PD-(D/E)XK superfamily using Support Vector Machines trained on data derived from profile-profile alignments. Using a number of both superfamily-specific and general features, SVMs were trained to identify true positive alignments of PD-(D/E)XK representatives.

::DEVELOPER

VU Institute of Biotechnology

:: SCREENSHOTS

N/A

::REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Laganeckas M., Margelevičius M., Venclovas Č. (2010)
Identification of new homologs of PD-(D/E)XK nucleases by Support Vector Machines trained on data derived from profile-profile alignments.
Nucl. Acids Res. (2011) 39 (4): 1187-1196.

JPred 4 – Protein Secondary Structure Prediction Server

JPred 4

:: DESCRIPTION

JPred is a Protein Secondary Structure Prediction server. JPred incorporates the Jnet algorithm in order to make more accurate predictions. In addition to protein secondary structure JPred also makes predictions on Solvent Accessibility and Coiled-coil regions (Lupas method).

:: DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2015 Apr 16. pii: gkv332.
JPred4: a protein secondary structure prediction server.
Drozdetskiy A, Cole C, Procter J, Barton GJ.

Cyscon 20150927 – Disulfide Connectivity Prediction Server

Cyscon 20150927

:: DESCRIPTION

Cyscon is a new hierarchical order reduction protocol for disulfide-bonding prediction.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

Accurate disulfide-bonding network predictions improve ab initio structure prediction of cysteine-rich proteins.
Yang J, He BJ, Jang R, Zhang Y, Shen HB.
Bioinformatics. 2015 Aug 7. pii: btv459.