To obtain a more complete sequence of a draft genome, its contigs usually are ordered .. Supplementary Data are available at NAR Online. DNA Dragon Contig Assembler assembles sequences, trace data (ABI, SCF, AB1 ), DNA sequences into contigs and allows a direct comparision of trace date. GenBank is part of the International Nucleotide Sequence Database to the most up-to-date and comprehensive DNA sequence information.
The availability of complete genomes is important to the analysis and interpretation of sequence data in many biological applications 3. In principle, the more contigs a draft genome has, the more difficult its downstream analysis becomes.
To obtain a more complete sequence of a draft genome, its contigs usually are ordered and oriented into larger gap-containing sequences, called scaffolds, so that the gaps between scaffolded contigs can be filled in the subsequent gap-closing process. In the scaffolding process, an available genomic sequence from a related organism can be used as a reference or template to order and orient the contigs in a draft genome.
Currently, many such reference-based scaffolding tools are available 4— In principle, the methods behind all these scaffolders fall into two main categories: The alignment-based scaffolding algorithms first align contigs or contig ends of a draft genome against a reference sequence and then try to scaffold the contigs according to the positions of their matches in the reference.
By considering genomic structures, the rearrangement-based scaffolding algorithms utilize a reference genome to scaffold the contigs of a draft genome in a way such that the orders of conserved genes or genomic markers between the scaffolded draft genome and the reference genome are as similar as possible.
In fact, only a few of all the reference-based scaffolders mentioned above allow the used reference genomes to be incomplete or unfinishedsuch as Projector 2 4OSLay 5Mauve Aligner 7 and r2cat 8. As mentioned before, most sequenced genomes are just draft 13 and hence complete reference genomes may not be always available for a draft genome to be scaffolded.
We have also used several real datasets to show that CSAR indeed outperforms other similar tools Projector2, OSLay and Mauve Aligner in terms of many evaluation metrics, such as sensitivity, precision, F-score, genome coverage, NGA50 and running time.Introduction to genome assembly
By considering contigs as linear chromosomes and the scaffolding of two contigs as a fusion to join these two contigs into a larger one, we formulated the scaffolding problem as a genome rearrangement problem as follows. A genomic marker or gene is an oriented sequence of DNA that starts with a tail and ends with a head.
Since a genomic marker can be present in two orientations i. In this way, a chromosome can be represented by a sequence of ordered genomic markers and a genome by a set of chromosomes. For our purpose, we represent a linear chromosome e. Van Domselaar et al. It's purpose is to allow research groups with small to intermediate amounts of eukaryotic and prokaryotic genome sequence i.
BAC clones, small whole genomes, preliminary sequencing data, etc. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. GenSAS - Genome Sequence Annotation Server - provides a one-stop website with a single graphical interface for running multiple structural and functional annotation tools, enabling visualization and manual curation of genome sequences.
Users can upload sequences into their account and run gene prediction programs, protein homology searches, map ESTs, identify repeats, ORFs and SSRs with custom parameter settings.
Each analysis is displayed on separate tracks of the graphical interface with custom editabe tracks to select final annotation of features and create gff3 files for upload to genome browsers such as GBrowse. Additional programs can be easily added using this Drupal based software. Genome-specific features identified by VIGOR include frameshifts, ribosomal slippage, RNA editing, stop codon read-through, overlapping genes, embedded genes, and mature peptide cleavage sites.
Genotyping capability for influenza and rotavirus is built into the program. BMC Bioinformatics It can validate and predict protein sequences encoded by an input flu sequence.
Web Server issue CpGAVAS Chloroplast Genome Annotation, Visualization, Analysis and GenBank Submission Tool - allows accurate chloroplast genome annotation, the generation of circular maps, the provision of useful analysis results of the annotated genome, the creation of files that can be submitted to GenBank directly. BAGEL Groningen Biomolecular Sciences and Biotechnology Institute, Haren, the Netherlands - will determine from an existing or non submitted GenBank file the presence of bacteriocins based on a database containing information of known bacteriocins and adjacent genes involved in bacteriocin activity.
This tool can be seen as a preliminary step before the functional re-annotation step to check quickly for missing or wrongly annotated genes. It worked nicely with phage genomes from kb.
A complete description of each terminator including a diagram is produced by this program. If you click on the "search for attenuators" it finds terminators and antiterminators. Nucleic Acids Research The size of input file is now limited to 50MB Reference: It provides annotation of sequence fragments, their phylogenetic classification and an initial metabolic reconstruction. The service also provides means for comparing phylogenetic classifications and metabolic reconstructions of metagenomes Reference: One of the problems with GenBank is that scientists do not update their submission data nor correct errors.
Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank but, from my perspective, it is not easy to use. In its absence I recommend the perl script gbf2tbl. Specialized annotation - general PlasmidFinder 1.
The method uses BLAST for identification of replicons of plasmids belonging to the major incompatibility Inc groups of Enterobacteriaceae. As input, the method can use both pre-assembled, complete or partial genomes, and short sequence reads from four different sequencing platforms.
DNA Dragon: DNA Sequence Contig Assembly Software
Carattoli A et al. All that is needed is the proteome of the phage to be classified and PHACTS will predict the lifestyle of that phage and return a confidence value for that prediction. The prediction is based on the 16S rRNA gene.
The prediction is based on the number of co-occurring k-mers substrings of k nucleotides in DNA sequence data, in this case mers between the genomes of reference bacteria in a database and the genome provided by the user. Hasman H et al. Larsen MV et al. In detail, it serves two particular purposes: The latter refers to source tracking i. Feng, Nucleic Acids Research.
In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Google Chrome is recommended; Firefox is also supported but the SVG visualizations within this app may not be as responsive.
Internet Explorer is unsupported. FSFinder2 Frameshift Signal Finder - Programmed ribosomal frameshifting is involved in the expression of certain genes from a wide range of organisms such as virus, bacteria and eukaryotes including human.
DNA Dragon - DNA Sequence Contig Assembler Software
In programmed frameshifting, the ribosome switches to an alternative frame at a specific site in response to a special signal in a messanger RNA. Programmed frameshift plays role in viral particle morphogenesis, autogenous control, and alternative enzymatic activities. The common frameshift is a -1 frameshift, in which the ribosome shifts a single nucleotide in the upstream direction. The major elements of -1 frameshifting consist of a slippery site, where the ribosome changes reading frames, and a stimulatory RNA structure such as pseudoknot or stem-loop located a few nucleotides downstream.
Protein splicing results in a native peptide bond between the ligated exteins. Two-component and other regulatory proteins: RPs identified in this manner are categorised into families, unambiguously annotated. Barakat M, et al. TCSs are comprised of a receptor histidine kinase HK and a partner response regulator RR and control important prokaryotic behaviors.
Each COG consists of a group of proteins found to be orthologous across at least three lineages and likely corresponds to an ancient conserved domain CloVR. Sites which offer this analysis include: Aziz RK et al. Van Domselaar GH et al. Markowitz VM et al. Powell S et al. Fischer S et al. Curr Protoc Bioinformatics; Chapter 6: Moriya Y et al. Specialized annotation - antibiotic resistance. ResFinder Acquired antimicrobial resistance gene finder - uses BLAST for identification of acquired antimicrobial resistance genes in whole-genome data.
Zankari E et al. Nucleic Acids Research, In BacMet version 1. CRISPRmap -provides a quick and detailed insight into repeat conservation and diversity of both bacterial and archaeal systems. It comprises the largest dataset of CRISPRs to date and enables comprehensive independent clustering analyses to determine conserved sequence families, potential structure motifs for endoribonucleases, and evolutionary relationships. A user-friendly web interface with many graphical tools and functions allows users to extract results, find CRISPR in personal sequences or calculate sequence similarity with spacers.
Rousseau C et al. This can be used to discover targets in newly sequenced genomic or metagenomic data. Biswas A et al.
After checks for potential off-target matches, the resulting sgRNA sequences are displayed graphically and can be exported to text files. Synthetic and Systems Biotechnology 1 2: Specialized annotation - virulence determinants: This is of particular interest to those working on bacteriophages for therapy VirulenceFinder Danish Technical University — identification of virulence genes.
The method is being extended to also include virulence genes for Enterococcus and Staphylococcus aureus. For each protein, additional information is presented including the presence of a signal peptide, the number of cysteine residues and the associated functional annotations.
The database currently houses 3, toxins which are linked to 1, corresponding toxin target records. Each toxin record ToxCard contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information.
Lim E et al. DBETH Database of Bacterial ExoToxins for Humans is a database of sequences, structures, interaction networks and analytical results for exotoxins, from 26 different human pathogenic bacterial genus.
All toxins are classified into 24 different Toxin classes. Chakraborty A et al. VFDB - is an integrated and comprehensive database of virulence factors for bacterial pathogens also including Chlamydia and Mycoplasma. While PAIs promote disease development, REIs give a fitness advantage to the host against multiple antimicrobial agents.