WebPHYLIP: a web interface to PHYLIP

A web interface to PHYLIP (version 3.57 C) is implemented using CGI/Perl programming. It enables users to do phylogenetic analysis through the Internet.     

wEMBOSS: a web interface for EMBOSS

SUMMARY: wEMBOSS provides a web environment from which the user can access EMBOSS in a user-friendly way. wEMBOSS supplies each user with space and tools to organize and review his or her work. AVAILABILITY: wEMBOSS can be downloaded at http://www.wemboss.org CONTACT: msarachu@biol.unlp.edu.ar.     

Using threatened plant species to identify conservation gaps and opportunities on the island of Cyprus

The cornerstone of EU nature conservation, the Natura 2000 (N2K) network is far from complete in many EU countries, including Cyprus, particularly where new datasets have become available. Thus, an important question in conservation biology is how new data can be incorporated in an effort to redesign N2K where appropriate. We analyse the efficacy of the N2K network in Cyprus, a global biodiversity hotspot, for protecting threatened vascular plants. We used 252 species for which detailed distributional data were available and added new records for 168 species. Overlaying a 1 km² grid map for Cyprus we identified distributional hotspots of threatened species (sensu IUCN) and assessed their representation level within the N2K network. Based on new recorded data we propose IUCN status changes for 15 species. There were 60 hotspots identified (cells with more than 5 threatened species) in the central-west, south, southeast and north parts of the island. GIS analysis demonstrated that 145 out of 252 species (57.5%) occur within the N2K network, ranging from 4 to 100% of their occurrences. Τhe conservation gaps identified are related to 107 threatened species (42.5% of Red Data Book plants) which are either completely outside the N2K network or in those areas where EU legislation is not applicable due to the complex political situation on the island. The most important conservation opportunities are found in the northern part of the island, where the acquis communautaire is suspended and the UK Sovereign Base Areas, which are excluded from the Accession Treaty of Cyprus. In the area under the effective control of the Government of the Republic of Cyprus (CYGCA) there are only two important hotspots found outside the N2K network.     

ESEfinder: A web resource to identify exonic splicing enhancers

Point mutations frequently cause genetic diseases by disrupting the correct pattern of pre-mRNA splicing. The effect of a point mutation within a coding sequence is traditionally attributed to the deduced change in the corresponding amino acid. However, some point mutations can have much more severe effects on the structure of the encoded protein, for example when they inactivate an exonic splicing enhancer (ESE), thereby resulting in exon skipping. ESEs also appear to be especially important in exons that normally undergo alternative splicing. Different classes of ESE consensus motifs have been described, but they are not always easily identified. ESEfinder (http://exon.cshl.edu/ESE/) is a web-based resource that facilitates rapid analysis of exon sequences to identify putative ESEs responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements.     

TargetCompare: A web interface to compare simultaneous miRNAs targets

MicroRNAs (miRNAs) are small non-coding nucleotide sequences between 17 and 25 nucleotides in length that primarily function in the regulation of gene expression. A since miRNA has thousand of predict targets in a complex, regulatory cell signaling network. Therefore, it is of interest to study multiple target genes simultaneously. Hence, we describe a web tool (developed using Java programming language and MySQL database server) to analyse multiple targets of pre-selected miRNAs. We cross validated the tool in eight most highly expressed miRNAs in the antrum region of stomach. This helped to identify 43 potential genes that are target of at least six of the referred miRNAs. The developed tool aims to reduce the randomness and increase the chance of selecting strong candidate target genes and miRNAs responsible for playing important roles in the studied tissue.

Availability

http://lghm.ufpa.br/targetcompare     

TAD: a web interface and database for tissue microarrays

Tissue microarrays are increasingly important tools that bring high-throughput technology to traditional pathology laboratories. In many cases, each spot on a tissue microarray is scored by a skilled pathologist and recorded manually. TAD consists of an Active Server Page web interface to a relational database that automates recording scores and linking them with clinical data for future interpretation. TAD is an open source application that can be installed locally.     

Closing the gaps among a web of DNA repair disorders

As recently as six years ago, three human diseases with similar phenotypes were mistakenly believed to be caused by a single genetic defect. The three diseases, Ataxia-telangiectasia, Nijmegen breakage syndrome, and an AT-like disorder are now known, however, to have defects in three separate genes: ATM, NBS1, and MRE11. Furthermore, new recent studies have shown now that all three gene products interact; the ATM kinase phosphorylates NBS1, which, in turn, associates with MRE11 to regulate DNA repair. Remarkably or expectedly, depending on one's point of view, the similarity in disease phenotypes is evidently due to defects in a common DNA repair pathway.     

The ethical acceptability of animal experiments: a proposal for a system to support decision-making

We describe a system to support decision-making on the ethical acceptability of animal experiments for scientific researchers and others responsible for ethical decision-making in animal experiments. The system consists of eight steps. Each step contains a number of substantive questions or a computational rule, leading to a well-articulated moral judgment on specific animal experiments. The system comprises a number of moral assumptions and pre-emptive norms, but leaves enough room for moral discretion and personal responsibility. The general ethical ideas behind the moral choices and assumptions are sketched and potential objections to the overall approach are discussed.     

Anisotropic network model: systematic evaluation and a new web interface

MOTIVATION: The Anisotropic Network Model (ANM) is a simple yet powerful model for normal mode analysis of proteins. Despite its broad use for exploring biomolecular collective motions, ANM has not been systematically evaluated to date. A lack of a convenient interface has been an additional obstacle for easy usage. RESULTS: ANM has been evaluated on a large set of proteins to establish the optimal model parameters that achieve the highest correlation with experimental data and its limits of accuracy and applicability. Residue fluctuations in globular proteins are shown to be more accurately predicted than those in nonglobular proteins, and core residues are more accurately described than solvent-exposed ones. Significant improvement in agreement with experiments is observed with increase in the resolution of the examined structure. A new server for ANM calculations is presented, which offers flexible options for controlling model parameters and output formats, interactive animation of collective modes and advanced graphical features. AVAILABILITY: ANM server (http://www.ccbb.pitt.edu/anm)     

MutaProt: a web interface for structural analysis of point mutations

A web-based tool, termed 'MutaProt', is described which analyses pairs of PDB files whose members differ in one, or two, amino acids. MutaProt examines the micro environment surrounding the exchanged residue(s) and can be searched by specifying a PDB ID, keywords, or any pair of amino acids. Detailed information about accessibility of the exchanged residue(s) and its atomic contacts are provided based on CSU software (Sobolev et al., Bioinformatics, 15, 327-332, 1999). An interactive 3D presentation of the superimposed regions around the mutation(s) is included. MutaProt is updated weekly.     

SeqAnt: A web service to rapidly identify and annotate DNA sequence variations

Background  

The enormous throughput and low cost of second-generation sequencing platforms now allow research and clinical geneticists to routinely perform single experiments that identify tens of thousands to millions of variant sites. Existing methods to annotate variant sites using information from publicly available databases via web browsers are too slow to be useful for the large sequencing datasets being routinely generated by geneticists. Because sequence annotation of variant sites is required before functional characterization can proceed, the lack of a high-throughput pipeline to efficiently annotate variant sites can act as a significant bottleneck in genetics research.     

Model of outcomes of screening mammography: information to support informed choices

Objective To provide easy to use estimates of the benefits and harms of biennial screening mammography for women aged 40, 50, 60, and 70 years.Design Markov process model, with data from BreastScreen Australia, the Australian Institute of Health and Welfare, and the Australian Bureau of Statistics.Main outcome measure Age specific outcomes expressed per 1000 women over 10 years.Results For every 1000 women screened over 10 years, 167-251 (depending on age) receive an abnormal result; 56-64 of these women undergo at least one biopsy, 9-26 have an invasive cancer detected by screening, and 3-6 have ductal carcinoma in situ (DCIS) detected by screening. More breast cancers (both invasive and DCIS) are diagnosed among screened than unscreened women. For example, among 1000 women aged 50 who have five biennial screens, 33 breast cancers are diagnosed: 28 invasive cancers (18 detected at screening and 10 interval cancers) and five DCIS (all detected at screening). By comparison, among 1000 women aged 50 who decline screening, 20 cancers are diagnosed over 10 years. There are about 0.5, 2, 3, and 2 fewer deaths from breast cancer over 10 years per 1000 women aged 40, 50, 60, and 70, respectively, who choose to be screened compared with women who decline screening at times determined by relevant policy.Conclusion Benefits and harms of screening mammography are relatively finely balanced. Quantitative estimates such as these can be used to support individual informed choices about screening.     

ClusterDraw web server: a tool to identify and visualize clusters of binding motifs for transcription factors

ClusterDraw is a program aimed to identification of binding sites and binding-site clusters. Major difference of the ClusterDraw from existing tools is its ability to scan a wide range of parameter values and weigh statistical significance of all possible clusters, smaller than a selected size. The program produces graphs along with decorated FASTA files. ClusterDraw web server is available at the following URL: http://flydev.berkeley.edu/cgi-bin/cld/submit.cgi     

Governance and forest landscape restoration: A framework to support decision-making

Governance challenges are frequently underestimated in forest landscape restoration. Forest restoration practitioners are generally foresters or ecologists and their focus tends to be limited to the specific restoration interventions themselves, such as removing exotic species, protecting sites for natural regeneration and re-planting indigenous trees. Indeed there are many technical challenges, unknowns in technical aspects of forest landscape restoration and knowledge gaps. However, and even more so when dealing with large scales, additional challenges that fall under the governance umbrella such as tenure, policy measures and institutions have a significant impact on restoration, influencing it either positively or negatively. Conversely, the landscape-scale restoration work itself can influence and shape governance arrangements. This paper attempts to explore this wider relationship between large scale forest restoration − and specifically forest landscape restoration (FLR) − and governance. It is intended to assist and provide guidance to forest landscape restoration practitioners, researchers and policymakers on the consideration and importance of governance, and alternative ways in which the two-way relationship (between governance and FLR) plays out. A framework is proposed to support practitioners, researchers and decision-makers to address governance in forest landscape restoration.