Xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains

The Xylella fastidiosa comparative genomic database is a scientific resource with the aim to provide a user-friendly interface for accessing high-quality manually curated genomic annotation and comparative sequence analysis, as well as for identifying and mapping prophage-like elements, a marked feature of Xylella genomes. Here we describe a database and tools for exploring the biology of this important plant pathogen. The hallmarks of this database are the high quality genomic annotation, the functional and comparative genomic analysis and the identification and mapping of prophage-like elements. It is available from web site http://www.xylella.lncc.br.     

An automated protein annotation filter for integrating web-based annotation tools

A wide range of web based prediction and annotation tools are frequently used for determining protein function from sequence. However, parallel processing of sequences for annotation through web tools is not possible due to several constraints in functional programming for multiple queries. Here, we propose the development of APAF as an automated protein annotation filter to overcome some of these difficulties through an integrated approach.     

Otterlace软件在猪全基因组序列人工注释分析中的应用

2009年11月,美、英等国科学家宣布首次绘制出家猪的基因组草图。近两年,随着全基因组序列陆续释放,越来越多的测序片段得到正确拼接组装,从全基因组水平上对猪功能基因进行注释分析显得尤为迫切。文章以丝切蛋白1(Cofilin 1,CFL1)基因的注释过程为例,介绍了运用Sanger研究所开发的Otterlace软件对猪全基因组的免疫基因序列进行人工分析与注释。通过详细说明Zmap、Blixem和Dotter 3个注释工具的使用方法,并给出了注释过程的主要步骤,以期对Otterlace的应用起一个抛砖引玉的作用。运用Otterlace软件对243个免疫相关基因进行分析,其中180个基因得到完整或部分注释,这为后续深入开展这些基因的功能研究奠定了基础。     

PipTools: a computational toolkit to annotate and analyze pairwise comparisons of genomic sequences

Sequence conservation between species is useful both for locating coding regions of genes and for identifying functional noncoding segments. Hence interspecies alignment of genomic sequences is an important computational technique. However, its utility is limited without extensive annotation. We describe a suite of software tools, PipTools, and related programs that facilitate the annotation of genes and putative regulatory elements in pairwise alignments. The alignment server PipMaker uses the output of these tools to display detailed information needed to interpret alignments. These programs are provided in a portable format for use on common desktop computers and both the toolkit and the PipMaker server can be found at our Web site (http://bio.cse.psu.edu/). We illustrate the utility of the toolkit using annotation of a pairwise comparison of the mouse MHC class II and class III regions with orthologous human sequences and subsequently identify conserved, noncoding sequences that are DNase I hypersensitive sites in chromatin of mouse cells.     

CLAGen: a tool for clustering and annotating gene sequences using a suffix tree algorithm

Most multiple gene sequence alignment methods rely on conventions regarding the score of a multiple alignment in pairwise fashion. Therefore, as the number of sequences increases, the runtime of sequencing expands exponentially. In order to solve the problem, this paper presents a multiple sequence alignment method using a linear-time suffix tree algorithm to cluster similar sequences at one time without pairwise alignment. After searching for common subsequences, cross-matching common subsequences were generated, and sometimes inexact matching was found. So, a procedure aimed at masking the inexact cross-matching pairs was suggested here. In addition, BLAST was combined with a clustering tool in order to annotate the clusters generated by suffix tree clustering. The proposed method for clustering and annotating genes consists of the following steps: (1) construction of a suffix tree; (2) searching and overlapping common subsequences; (3) grouping subsequence pairs; (4) masking cross-matching pairs; (5) clustering gene sequences; (6) annotating gene clusters by the BLAST search. The performance of the proposed system, CLAGen, was successfully evaluated with 42 gene sequences in a TCA cycle (a citrate cycle) of bacteria. The system generated 11 clusters and found the longest subsequences of each cluster, which are biologically significant.     

Classifying genomic sequences by sequence feature analysis

Traditional sequence analysis depends on sequence alignment. In this study, we analyzed various functional regions of the human genome based on sequence features, including word frequency, dinucleotide relative abundance, and base-base correlation. We analyzed the human chromosome 22 and classified the upstream, exon, intron, downstream, and intergenic regions by principal component analysis and discriminant analysis of these features. The results show that we could classify the functional regions of genome based on sequence feature and discriminant analysis.     

Increased detection of structural templates using alignments of designed sequences

Protein structure prediction by comparative modeling benefits greatly from the use of multiple sequence alignment information to improve the accuracy of structural template identification and the alignment of target sequences to structural templates. Unfortunately, this benefit is limited to those protein sequences for which at least several natural sequence homologues exist. We show here that the use of large diverse alignments of computationally designed protein sequences confers many of the same benefits as natural sequences in identifying structural templates for comparative modeling targets. A large-scale massively parallelized application of an all-atom protein design algorithm, including a simple model of peptide backbone flexibility, has allowed us to generate 500 diverse, non-native, high-quality sequences for each of 264 protein structures in our test set. PSI-BLAST searches using the sequence profiles generated from the designed sequences ("reverse" BLAST searches) give near-perfect accuracy in identifying true structural homologues of the parent structure, with 54% coverage. In 41 of 49 genomes scanned using reverse BLAST searches, at least one novel structural template (not found by the standard method of PSI-BLAST against PDB) is identified. Further improvements in coverage, through optimizing the scoring function used to design sequences and continued application to new protein structures beyond the test set, will allow this method to mature into a useful strategy for identifying distantly related structural templates.     

GS-Aligner: a novel tool for aligning genomic sequences using bit-level operations

A novel algorithm, GS-Aligner, that uses bit-level operations was developed for aligning genomic sequences. GS-Aligner is efficient in terms of both time and space for aligning two very long genomic sequences and for identifying genomic rearrangements such as translocations and inversions. It is suitable for aligning fairly divergent sequences such as human and mouse genomic sequences. It consists of several efficient components: bit-level coding, search for matching segments between the two sequences as alignment anchors, longest increasing subsequence (LIS), and optimal local alignment. Efforts have been made to reduce the execution time of the program to make it truly practical for aligning very long sequences. Empirical tests suggest that for relatively divergent sequences such as sequences from different mammalian orders or from a mammal and a nonmammalian vertebrate GS-Aligner performs better than existing methods. The program and data can be downloaded from http://pondside.uchicago.edu/~lilab/ and http://webcollab.iis.sinica.edu.tw/~biocom.     

Extrachromosomal circular DNA derived from tandemly repeated genomic sequences in plants

Extrachromosomal circular DNA (eccDNA) is one characteristic of the plasticity of the eukaryotic genome. It was found in various non-plant organisms from yeast to humans. EccDNA is heterogeneous in size and contains sequences derived primarily from repetitive chromosomal DNA. Here, we report the occurrence of eccDNA in small and large genome plant species, as identified using two-dimensional gel electrophoresis. We show that eccDNA is readily detected in both Arabidopsis thaliana and Brachycome dichromosomatica , reflecting a normal phenomenon that occurs in wild-type plants. The size of plant eccDNA ranges from > 2 kb to < 20 kb, which is similar to the sizes found in other organisms. These DNA molecules correspond to 5S ribosomal DNA (rDNA), non-coding chromosomal high-copy tandem repeats and telomeric DNA of both species. Circular multimers of the repeating unit of 5S rDNA were identified in both species. In addition, similar multimers were also demonstrated with the B. dichromosomatica repetitive element Bdm29. Such circular multimers of tandem repeats were found in animal models, suggesting a common mechanism for eccDNA formation among eukaryotes. This mechanism may involve looping-out via intrachromosomal homologous recombination. The implications of these results on genome plasticity and evolutionary processes are discussed.     

TheViral MetaGenome Annotation Pipeline(VMGAP):an automated tool for the functional annotation of viral Metagenomic shotgun sequencing data

In the past few years, the field of metagenomics has been growing at an accelerated pace, particularly in response to advancements in new sequencing technologies. The large volume of sequence data from novel organisms generated by metagenomic projects has triggered the development of specialized databases and tools focused on particular groups of organisms or data types. Here we describe a pipeline for the functional annotation of viral metagenomic sequence data. The Viral MetaGenome Annotation Pipeline (VMGAP) pipeline takes advantage of a number of specialized databases, such as collections of mobile genetic elements and environmental metagenomes to improve the classification and functional prediction of viral gene products. The pipeline assigns a functional term to each predicted protein sequence following a suite of comprehensive analyses whose results are ranked according to a priority rules hierarchy. Additional annotation is provided in the form of enzyme commission (EC) numbers, GO/MeGO terms and Hidden Markov Models together with supporting evidence.     

A novel class of small repetitive DNA sequences in Enterococcus faecalis

The structural organization of Enterococcus faecalis repeats (EFAR) is described, palindromic DNA sequences identified in the genome of the Enterococcus faecalis V583 strain by in silico analyses. EFAR are a novel type of miniature insertion sequences, which vary in size from 42 to 650 bp. Length heterogeneity results from the variable assembly of 16 different sequence types. Most elements measure 170 bp, and can fold into peculiar L-shaped structures resulting from the folding of two independent stem-loop structures (SLSs). Homologous chromosomal regions lacking or containing EFAR sequences were identified by PCR among 20 E. faecalis clinical isolates of different genotypes. Sequencing of a representative set of 'empty' sites revealed that 24-37 bp-long sequences, unrelated to each other but all able to fold into SLSs, functioned as targets for the integration of EFAR. In the process, most of the SLS had been deleted, but part of the targeted stems had been retained at EFAR termini.     

Functional modelling of an equine bronchoalveolar lavage fluid proteome provides experimental confirmation and functional annotation of equine genome sequences

The equine genome sequence enables the use of high-throughput genomic technologies in equine research, but accurate identification of expressed gene products and interpreting their biological relevance require additional structural and functional genome annotation. Here, we employ the equine genome sequence to identify predicted and known proteins using proteomics and model these proteins into biological pathways, identifying 582 proteins in normal cell-free equine bronchoalveolar lavage fluid (BALF). We improved structural and functional annotation by directly confirming the in vivo expression of 558 (96%) proteins, which were computationally predicted previously, and adding Gene Ontology (GO) annotations for 174 proteins, 108 of which lacked functional annotation. Bronchoalveolar lavage is commonly used to investigate equine respiratory disease, leading us to model the associated proteome and its biological functions. Modelling of protein functions using Ingenuity Pathway Analysis identified carbohydrate metabolism, cell-to-cell signalling, cellular function, inflammatory response, organ morphology, lipid metabolism and cellular movement as key biological processes in normal equine BALF. Comparative modelling of protein functions in normal cell-free bronchoalveolar lavage proteomes from horse, human, and mouse, performed by grouping GO terms sharing common ancestor terms, confirms conservation of functions across species. Ninety-one of 92 human GO categories and 105 of 109 mouse GO categories were conserved in the horse. Our approach confirms the utility of the equine genome sequence to characterize protein networks without antibodies or mRNA quantification, highlights the need for continued structural and functional annotation of the equine genome and provides a framework for equine researchers to aid in the annotation effort.     

Discovering and detecting transposable elements in genome sequences

The contribution of transposable elements (TEs) to genome structure and evolution as well as their impact on genome sequencing, assembly, annotation and alignment has generated increasing interest in developing new methods for their computational analysis. Here we review the diversity of innovative approaches to identify and annotate TEs in the post-genomic era, covering both the discovery of new TE families and the detection of individual TE copies in genome sequences. These approaches span a broad spectrum in computational biology including de novo, homology-based, structure-based and comparative genomic methods. We conclude that the integration and visualization of multiple approaches and the development of new conceptual representations for TE annotation will further advance the computational analysis of this dynamic component of the genome.     

MitoBamAnnotator: A web-based tool for detecting and annotating heteroplasmy in human mitochondrial DNA sequences

The use of Next-Generation Sequencing of mitochondrial DNA is becoming widespread in biological and clinical research. This, in turn, creates a need for a convenient tool that detects and analyzes heteroplasmy. Here we present MitoBamAnnotator, a user friendly web-based tool that allows maximum flexibility and control in heteroplasmy research. MitoBamAnnotator provides the user with a comprehensively annotated overview of mitochondrial genetic variation, allowing for an in-depth analysis with no prior knowledge in programming.     

一个园艺植物基因组序列和注释的在线批量实时提取平台

目前, 大量园艺植物基因组测序已经完成或接近尾声, 它们的基因组序列和注释数据极大地促进了功能基因组学研究。为给科研人员提供批量下载特定的基因组区段序列和注释平台, 笔者开发了一个称为OBRRP的生物信息学工具。OBRRP具有提取葡萄(Vitis vinifera)、桃(Prunus persica)、草莓(Fragaria vesca)、黄瓜(Cucumis sativus)、西瓜(Citrullus lanatus)、番茄(Solanum lycopersicum)、甜橙(Citrus sinensis)、苹果(Malus x domestica)、猕猴桃(Actinidia chinensis)、马铃薯(Solanum tuberosum)、香蕉(Musa acuminata)和拟南芥(Arabidopsis thaliana) 12种植物基因组序列及注释数据的功能; 同时, 也具有扩展到其它Gbrowser浏览器架构的数据库功能。测试结果表明, OBRRP是一个快捷简便的在线、批量和实时提取工具, 其登录地址为http://bioinfo.jit.edu.cn/OBRRP/。     

Conversion of nucleotides sequences into genomic signals

An original tetrahedral representation of the Genetic Code (GC) that better describes its structure, degeneration and evolution trends is defined. The possibility to reduce the dimension of the representation by projecting the GC tetrahedron on an adequately oriented plane is also analyzed, leading to some equivalent complex representations of the GC. On these bases, optimal symbolic-to-digital mappings of the linear, nucleic acid strands into real or complex genomic signals are derived at nucleotide, codon and amino acid levels. By converting the sequences of nucleotides and polypeptides into digital genomic signals, this approach offers the possibility to use a large variety of signal processing methods for their handling and analysis. It is also shown that some essential features of the nucleotide sequences can be better extracted using this representation. Specifically, the paper reports for the first time the existence of a global helicoidal wrapping of the complex representations of the bases along DNA sequences, a large scale trend of genomic signals. New tools for genomic signal analysis, including the use of phase, aggregated phase, unwrapped phase, sequence path, stem representation of components'relative frequencies, as well as analysis of the transitions are introduced at the nucleotide, codon and amino acid levels, and in a multiresolution approach.     

New local potential useful for genome annotation and 3D modeling

A new potential energy function representing the conformational preferences of sequentially local regions of a protein backbone is presented. This potential is derived from secondary structure probabilities such as those produced by neural network-based prediction methods. The potential is applied to the problem of remote homolog identification, in combination with a distance-dependent inter-residue potential and position-based scoring matrices. This fold recognition jury is implemented in a Java application called JThread. These methods are benchmarked on several test sets, including one released entirely after development and parameterization of JThread. In benchmark tests to identify known folds structurally similar to (but not identical with) the native structure of a sequence, JThread performs significantly better than PSI-BLAST, with 10% more structures identified correctly as the most likely structural match in a fold library, and 20% more structures correctly narrowed down to a set of five possible candidates. JThread also improves the average sequence alignment accuracy significantly, from 53% to 62% of residues aligned correctly. Reliable fold assignments and alignments are identified, making the method useful for genome annotation. JThread is applied to predicted open reading frames (ORFs) from the genomes of Mycoplasma genitalium and Drosophila melanogaster, identifying 20 new structural annotations in the former and 801 in the latter.