RESCRIPt 2021.8.0 – REference Sequence annotation and CuRatIon Pipeline

RESCRIPt 2021.8.0

:: DESCRIPTION

RESCRIPt is a Python 3 software package and QIIME 2 plugin for reproducible generation and management of reference sequence taxonomy databases, including dedicated functions that streamline creating databases from popular sources, and functions for evaluating, comparing, and interactively exploring qualitative and quantitative characteristics across reference databases.

::DEVELOPER

Laboratory of Food Systems Biotechnology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Python
QIIME
conda

:: DOWNLOAD

RESCRIPt

:: MORE INFORMATION

Citation:

Robeson MS 2nd, O’Rourke DR, Kaehler BD, Ziemski M, Dillon MR, Foster JT, Bokulich NA.
RESCRIPt: Reproducible sequence taxonomy reference database management.
PLoS Comput Biol. 2021 Nov 8;17(11):e1009581. doi: 10.1371/journal.pcbi.1009581. Epub ahead of print. PMID: 34748542.

HRIBO 1.5.1 – High-throughput Annotation by Ribo-seq

HRIBO 1.5.1

:: DESCRIPTION

HRIBO is a workflow to enable reproducible and high-throughput analysis of bacterial Ribo-seq data. The workflow performs all required pre-processing steps and quality control. Importantly, HRIBO outputs annotation-independent ORF predictions based on two complementary prokaryotic-focused tools, and integrates them with additional computed features. This facilitates both the rapid discovery of ORFs and their prioritization for functional characterization.

::DEVELOPER

HRIBO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Conda

:: DOWNLOAD

HRIBO

:: MORE INFORMATION

Citation

Gelhausen R, Svensson SL, Froschauer K, Heyl F, Hadjeras L, Sharma CM, Eggenhofer F, Backofen R.
HRIBO: high-throughput analysis of bacterial ribosome profiling data.
Bioinformatics. 2021 Aug 4;37(14):2061-2063. doi: 10.1093/bioinformatics/btaa959. Erratum in: Bioinformatics. 2021 Jul 16;: PMID: 33175953; PMCID: PMC8337001.

CRISPRloci – Annotation of CRISPR-Cas Systems

CRISPRloci

:: DESCRIPTION

CRISPRloci provides an automated and comprehensive in silico characterization of CRISPR-Cas system on bacterial and archaeal genomes. It is a full suite for CRISPR locus characteriztion that includes CRISPR array orientation, detection of conserved leaders, cas gene annotation and subtype classification.

::DEVELOPER

Bioinformatics Group Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

CRISPRloci

:: MORE INFORMATION

Citation

Alkhnbashi OS, Mitrofanov A, Bonidia R, Raden M, Tran VD, Eggenhofer F, Shah SA, Öztürk E, Padilha VA, Sanches DS, de Carvalho ACPLF, Backofen R.
CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas systems.
Nucleic Acids Res. 2021 Jul 2;49(W1):W125-W130. doi: 10.1093/nar/gkab456. PMID: 34133710; PMCID: PMC8265192.

ASA3P v1.3.0 – Automatic Bacterial Isolate Assembly, Annotation and Analyses Pipeline

ASA3P v1.3.0

:: DESCRIPTION

ASA3P is an automatic and highly scalable assembly, annotation and higher-level analyses pipeline for closely related bacterial isolates.

::DEVELOPER

Bioinformatics and Systems Biology, Justus-Liebig-University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Docker / OpenStack

:: DOWNLOAD

ASA3P

:: MORE INFORMATION

Citation

Schwengers O, Hoek A, Fritzenwanker M, Falgenhauer L, Hain T, Chakraborty T, Goesmann A.
ASA3P: An automatic and scalable pipeline for the assembly, annotation and higher-level analysis of closely related bacterial isolates.
PLoS Comput Biol. 2020 Mar 5;16(3):e1007134. doi: 10.1371/journal.pcbi.1007134. PMID: 32134915; PMCID: PMC7077848.

Bakta 1.2.2 – Rapid & Standardized Annotation of Bacterial Genomes & Plasmids

Bakta 1.2.2

:: DESCRIPTION

Bakta is a tool for the rapid & standardized annotation of bacterial genomes & plasmids.

::DEVELOPER

Bioinformatics and Systems Biology, Justus-Liebig-University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

Bakta

:: MORE INFORMATION

Citation

Schwengers O, Jelonek L, Dieckmann MA, Beyvers S, Blom J, Goesmann A.
Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification.
Microb Genom. 2021 Nov;7(11). doi: 10.1099/mgen.0.000685. PMID: 34739369.

iwa-miRNA – Interactive Annotation of Plant MiRNAs

iwa-miRNA

:: DESCRIPTION

iwa-miRNA is a web-based platform for interactive annotation of plant miRNAs.

::DEVELOPER

Ma Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

iwa-miRNA

:: MORE INFORMATION

Citation

Zhang T, Zhai J, Zhang X, Ling L, Li M, Xie S, Song M, Ma C.
Interactive Web-based Annotation of Plant MicroRNAs with iwa-miRNA.
Genomics Proteomics Bioinformatics. 2021 Jul 28:S1672-0229(21)00161-3. doi: 10.1016/j.gpb.2021.02.010. Epub ahead of print. PMID: 34332120.

mVISTA – Compare Sequences & Visualize Alignments with Annotation Information

mVISTA

:: DESCRIPTION

mVISTA is a set of programs for comparing DNA sequences from two or more species up to megabases long and visualize these alignments with annotation information. mVISTA has a clean output, allowing for easy identification of sequence similarities and differences, and is easily configurable, enabling the visualization of alignments of various lengths at different levels of resolution. It is implemented as an on-line server that provides access to global pairwise, multiple and glocal (global with rearrangements) alignment tools.

mVISTA web version

::DEVELOPER

Genomics Division of Lawrence Berkeley National Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Mac OsX / Linux
JAVA

:: DOWNLOAD

mVISTA

:: MORE INFORMATION

mVISTA and Avid are free for academic or non-profit research institutions to use for internal research purposes. Commercial companies may submit sequences over the Web using the VISTA web site at no charge. To obtain a copy of mVISTA or Avid for internal use, commercial entities are required to purchase a site license for commercial use.

Citation:

Frazer KA, Pachter L, Poliakov A, Rubin EM, Dubchak I. VISTA: computational tools for comparative genomics. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9

Mayor C., Brudno M., Schwartz J. R., Poliakov A., Rubin E. M., Frazer K. A., Pachter L. S. and Dubchak I. (2000) VISTA: Visualizing Global DNA Sequence Alignments of Arbitrary Length. Bioinformatics, 16:1046.

TSSAR 1.0.1 – Transcription Start Site Annotation Regime

TSSAR 1.0.1

:: DESCRIPTION

TSSAR is a Web Service for predicting bacterial Transcription Start Sites from dRNA-seq data. It is built on a RESTful Client/Server architecture that allows for rapid screening and processing of Next-Generation Sequencing data.

::DEVELOPER

Theoretical Biochemistry Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Mac OsX/ Windows
Java
R package

:: DOWNLOAD

TSSAR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Mar 27;15:89. doi: 10.1186/1471-2105-15-89.
TSSAR: TSS annotation regime for dRNA-seq data.
Amman F1, Wolfinger MT, Lorenz R, Hofacker IL, Stadler PF,Findeiß S.

KAAS 20140224 – KEGG Automatic Annotation Server

KAAS 20140224

:: DESCRIPTION

KAAS provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.

::DEVELOPER

Kyoto University Bioinformatics Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Perl
ruby
NCBI
HMMER

:: DOWNLOAD

KAAS

:: MORE INFORMATION

Citation

KAAS: an automatic genome annotation and pathway reconstruction server.
Moriya Y, Itoh M, Okuda S, Yoshizawa AC, Kanehisa M.
Nucleic Acids Res. 2007 Jul;35(Web Server issue):W182-5.

REPET 3.0 / PASTEClassifier 2.0 – Detection, Annotation and Analysis of Repeats in Genomic Sequences

REPET 3.0 / PASTEClassifier 2.0

:: DESCRIPTION

REPET is a software of detection, annotation and analysis of repeats in genomic sequences, specifically designed for transposable elements

PASTEClassifier classifies TEs by searching for structural features and similarities.

::DEVELOPER

URGI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

REPET , PASTEC

:: MORE INFORMATION

Citation

PASTEC: An Automatic Transposable Element Classification Tool.
Hoede C, Arnoux S, Moisset M, Chaumier T, Inizan O, Jamilloux V, Quesneville H.
PLoS One. 2014 May 2;9(5):e91929. doi: 10.1371/journal.pone.0091929.

Flutre T, Duprat E, Feuillet C, Quesneville H.
Considering transposable element diversification in de novo annotation approaches.
PLoS One. 2011 Jan 31;6(1):e16526.