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1.
Tayyaba Yasmin Inayat Ur Rehman Adnan Ahmad Ansari Khurrum liaqat Muhammad Irfan khan 《Bioinformation》2012,8(25):1277-1279
The availability of genomic sequences of many organisms has opened new challenges in many aspects particularly in terms of
genome analysis. Sequence extraction is a vital step and many tools have been developed to solve this issue. These tools are
available publically but have limitations with reference to the sequence extraction, length of the sequence to be extracted, organism
specificity and lack of user friendly interface. We have developed a java based software package having three modules which can
be used independently or sequentially. The tool efficiently extracts sequences from large datasets with few simple steps. It can
efficiently extract multiple sequences of any desired length from a genome of any organism. The results are crosschecked by
published data.
Availability
URL 1: http://ww3.comsats.edu.pk/bio/ResearchProjects.aspxURL 2: http://ww3.comsats.edu.pk/bio/SequenceManeuverer.aspx 相似文献2.
3.
We present an efficient computational architecture designed using supervised machine learning model to predict amyloid fibril
forming protein segments, named AmylPepPred. The proposed prediction model is based on bio-physio-chemical properties of
primary sequences and auto-correlation function of their amino acid indices. AmylPepPred provides a user friendly web interface
for the researchers to easily observe the fibril forming and non-fibril forming hexmers in a given protein sequence. We expect that
this stratagem will be highly encouraging in discovering fibril forming regions in proteins thereby benefit in finding therapeutic
agents that specifically aim these sequences for the inhibition and cure of amyloid illnesses.
Availability
AmylPepPred is available freely for academic use at www.zoommicro.in/amylpeppred 相似文献4.
Basic Local Alignment Search Tool, (BLAST) allows the comparison of a query sequence/s
to a database of sequences and identifies those sequences that are similar to the query above a
user-defined threshold. We have developed a user friendly web application, MULTBLAST that runs a
series of BLAST searches on a user-supplied list of proteins against one or more target protein or
nucleotide databases. The application pre-processes the data, launches each individual BLAST search
on the University of Nevada, Reno''s-TimeLogic DeCypher® system (available from
Active Motif, Inc.) and retrieves and combines all the results into a simple, easy to read output file.
The output file presents the list of the query proteins, followed by the BLAST results for the matching
sequences from each target database in consecutive columns. This format is especially useful for
either comparing the results from the different target databases, or analyzing the results while keeping
the identification of each target database separate.
Availability
The application is available at the URLhttp://blastpipe.biochem.unr.edu/ 相似文献5.
Background to the debate: Several studies have found disparities in the outcome of medical procedures across different hospitals—better outcomes have been associated with higher procedure volume. An Institute of Medicine workshop found such a “volume–outcome relationship” for two types of cancer surgery: resection of the pancreas and esophagus (http://www.iom.edu/?id=31508). This debate examines whether physicians have an ethical obligation to inform patients of hospital outcome disparities for these cancers. 相似文献
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Recent studies have revealed that a small non-coding RNA, microRNA (miRNA) down-regulates its mRNA targets. This effect is regarded as an important role in various biological processes. Many studies have been devoted to predicting miRNA-target interactions. These studies indicate that the interactions may only be functional in some specific tissues, which depend on the characteristics of an miRNA. No systematic methods have been established in the literature to investigate the correlation between miRNA-target interactions and tissue specificity through microarray data. In this study, we propose a method to investigate miRNA-target interaction-supported tissues, which is based on experimentally validated miRNA-target interactions. The tissue specificity results by our method are in accordance with the experimental results in the literature.
Availability and Implementation
Our analysis results are available at http://tsmti.mbc.nctu.edu.tw/ and http://www.stat.nctu.edu.tw/hwang/tsmti.html. 相似文献8.
Background
Many prediction tools for microRNA (miRNA) targets have been developed, but inconsistent predictions were observed across multiple algorithms, which can make further analysis difficult. Moreover, the nomenclature of human miRNAs changes rapidly. To address these issues, we developed a web-based system, miRSystem, for converting queried miRNAs to the latest annotation and predicting the function of miRNA by integrating miRNA target gene prediction and function/pathway analyses.Results
First, queried miRNA IDs were converted to the latest annotated version to prevent potential conflicts resulting from multiple aliases. Next, by combining seven algorithms and two validated databases, potential gene targets of miRNAs and their functions were predicted based on the consistency across independent algorithms and observed/expected ratios. Lastly, five pathway databases were included to characterize the enriched pathways of target genes through bootstrap approaches. Based on the enriched pathways of target genes, the functions of queried miRNAs could be predicted.Conclusions
MiRSystem is a user-friendly tool for predicting the target genes and their associated pathways for many miRNAs simultaneously. The web server and the documentation are freely available at http://mirsystem.cgm.ntu.edu.tw/. 相似文献9.
Background
Heme-copper oxygen reductases (HCOs) are the last enzymatic complexes of most aerobic respiratory chains, reducing dioxygen to water and translocating up to four protons across the inner mitochondrial membrane (eukaryotes) or cytoplasmatic membrane (prokaryotes). The number of completely sequenced genomes is expanding exponentially, and concomitantly, the number and taxonomic distribution of HCO sequences. These enzymes were initially classified into three different types being this classification recently challenged.Methodology
We reanalyzed the classification scheme and developed a new bioinformatics classifier for the HCO and Nitric oxide reductases (NOR), which we benchmark against a manually derived gold standard sequence set. It is able to classify any given sequence of subunit I from HCO and NOR with a global recall and precision both of 99.8%. We use this tool to classify this protein family in 552 completely sequenced genomes.Conclusions
We concluded that the new and broader data set supports three functional and evolutionary groups of HCOs. Homology between NORs and HCOs is shown and NORs closest relationship with C Type HCOs demonstrated. We established and made available a classification web tool and an integrated Heme-Copper Oxygen reductase and NOR protein database (www.evocell.org/hco). 相似文献10.
Motivation
Accurate identification of peptides binding to specific Major Histocompatibility Complex Class II (MHC-II) molecules is of great importance for elucidating the underlying mechanism of immune recognition, as well as for developing effective epitope-based vaccines and promising immunotherapies for many severe diseases. Due to extreme polymorphism of MHC-II alleles and the high cost of biochemical experiments, the development of computational methods for accurate prediction of binding peptides of MHC-II molecules, particularly for the ones with few or no experimental data, has become a topic of increasing interest. TEPITOPE is a well-used computational approach because of its good interpretability and relatively high performance. However, TEPITOPE can be applied to only 51 out of over 700 known HLA DR molecules.Method
We have developed a new method, called TEPITOPEpan, by extrapolating from the binding specificities of HLA DR molecules characterized by TEPITOPE to those uncharacterized. First, each HLA-DR binding pocket is represented by amino acid residues that have close contact with the corresponding peptide binding core residues. Then the pocket similarity between two HLA-DR molecules is calculated as the sequence similarity of the residues. Finally, for an uncharacterized HLA-DR molecule, the binding specificity of each pocket is computed as a weighted average in pocket binding specificities over HLA-DR molecules characterized by TEPITOPE.Result
The performance of TEPITOPEpan has been extensively evaluated using various data sets from different viewpoints: predicting MHC binding peptides, identifying HLA ligands and T-cell epitopes and recognizing binding cores. Among the four state-of-the-art competing pan-specific methods, for predicting binding specificities of unknown HLA-DR molecules, TEPITOPEpan was roughly the second best method next to NETMHCIIpan-2.0. Additionally, TEPITOPEpan achieved the best performance in recognizing binding cores. We further analyzed the motifs detected by TEPITOPEpan, examining the corresponding literature of immunology. Its online server and PSSMs therein are available at http://www.biokdd.fudan.edu.cn/Service/TEPITOPEpan/. 相似文献11.
Background
The composition vector (CV) method has been proved to be a reliable and fast alignment-free method to analyze large COI barcoding data. In this study, we modify this method for analyzing multi-gene datasets for plant DNA barcoding. The modified method includes an adjustable-weighted algorithm for the vector distance according to the ratio in sequence length of the candidate genes for each pair of taxa.Methodology/Principal Findings
Three datasets, matK+rbcL dataset with 2,083 sequences, matK+rbcL dataset with 397 sequences and matK+rbcL+trnH-psbA dataset with 397 sequences, were tested. We showed that the success rates of grouping sequences at the genus/species level based on this modified CV approach are always higher than those based on the traditional K2P/NJ method. For the matK+rbcL datasets, the modified CV approach outperformed the K2P-NJ approach by 7.9% in both the 2,083-sequence and 397-sequence datasets, and for the matK+rbcL+trnH-psbA dataset, the CV approach outperformed the traditional approach by 16.7%.Conclusions
We conclude that the modified CV approach is an efficient method for analyzing large multi-gene datasets for plant DNA barcoding. Source code, implemented in C++ and supported on MS Windows, is freely available for download at http://math.xtu.edu.cn/myphp/math/research/source/Barcode_source_codes.zip. 相似文献12.
Ashish Kumar Tewari Rashi Gulshan Wadhwa Sanjeev Kumar Sharma Chakresh Kumar Jain 《Bioinformation》2013,9(2):112-115
Bioterrorism is the intended use of pathogenic strains of microbes to widen terror in a population. There is a definite need to
promote research for development of vaccines, therapeutics and diagnostic methods as a part of preparedness to any bioterror
attack in the future. BIRS is an open-access database of collective information on the organisms related to bioterrorism. The
architecture of database utilizes the current open-source technology viz PHP ver 5.3.19, MySQL and IIS server under windows
platform for database designing. Database stores information on literature, generic- information and unique pathways of about 10
microorganisms involved in bioterrorism. This may serve as a collective repository to accelerate the drug discovery and vaccines
designing process against such bioterrorist agents (microbes). The available data has been validated from various online resources
and literature mining in order to provide the user with a comprehensive information system.
Availability
The database is freely available at http://www.bioterrorism.biowaves.org 相似文献13.
14.
Chinnaiah Swaminathan Vinobha Maruthamuthu Rajadurai Ekambaram Rajasekaran 《Bioinformation》2008,3(2):98-99
The use of bioinformatics tools require different sequence formats at various instances. Every tool uses specific set of
formats for processing. Sequence in one format is often required in another format. Thus, there is a need for sequence
format conversion. A number of such tools are available in the public domain. Here, we describe BIOFFORC as a file format
converter. The tool is developed with a graphical user interface in PERL.
Availability
http://www.winningpath.com/biofforc/ 相似文献15.
Background
DNA barcoding is one means of establishing a rapid, accurate, and cost-effective system for the identification of species. It involves the use of short, standard gene targets to create sequence profiles of known species against sequences of unknowns that can be matched and subsequently identified. The Fish Barcode of Life (FISH-BOL) campaign has the primary goal of gathering DNA barcode records for all the world''s fish species. As a contribution to FISH-BOL, we examined the degree to which DNA barcoding can discriminate marine fishes from the South China Sea.Methodology/Principal Findings
DNA barcodes of cytochrome oxidase subunit I (COI) were characterized using 1336 specimens that belong to 242 species fishes from the South China Sea. All specimen provenance data (including digital specimen images and geospatial coordinates of collection localities) and collateral sequence information were assembled using Barcode of Life Data System (BOLD; www.barcodinglife.org). Small intraspecific and large interspecific differences create distinct genetic boundaries among most species. In addition, the efficiency of two mitochondrial genes, 16S rRNA (16S) and cytochrome b (cytb), and one nuclear ribosomal gene, 18S rRNA (18S), was also evaluated for a few select groups of species.Conclusions/Significance
The present study provides evidence for the effectiveness of DNA barcoding as a tool for monitoring marine biodiversity. Open access data of fishes from the South China Sea can benefit relative applications in ecology and taxonomy. 相似文献16.
jMOTU and Taxonerator: turning DNA Barcode sequences into annotated operational taxonomic units 总被引:1,自引:0,他引:1
Background
DNA barcoding and other DNA sequence-based techniques for investigating and estimating biodiversity require explicit methods for associating individual sequences with taxa, as it is at the taxon level that biodiversity is assessed. For many projects, the bioinformatic analyses required pose problems for laboratories whose prime expertise is not in bioinformatics. User-friendly tools are required for both clustering sequences into molecular operational taxonomic units (MOTU) and for associating these MOTU with known organismal taxonomies.Results
Here we present jMOTU, a Java program for the analysis of DNA barcode datasets that uses an explicit, determinate algorithm to define MOTU. We demonstrate its usefulness for both individual specimen-based Sanger sequencing surveys and bulk-environment metagenetic surveys using long-read next-generation sequencing data. jMOTU is driven through a graphical user interface, and can analyse tens of thousands of sequences in a short time on a desktop computer. A companion program, Taxonerator, that adds traditional taxonomic annotation to MOTU, is also presented. Clustering and taxonomic annotation data are stored in a relational database, and are thus amenable to subsequent data mining and web presentation.Conclusions
jMOTU efficiently and robustly identifies the molecular taxa present in survey datasets, and Taxonerator decorates the MOTU with putative identifications. jMOTU and Taxonerator are freely available from http://www.nematodes.org/. 相似文献17.
Background
B-cell epitopes have been studied extensively due to their immunological applications, such as peptide-based vaccine development, antibody production, and disease diagnosis and therapy. Despite several decades of research, the accurate prediction of linear B-cell epitopes has remained a challenging task.Results
In this work, based on the antigen’s primary sequence information, a novel linear B-cell epitope prediction model was developed using the multiple linear regression (MLR). A 10-fold cross-validation test on a large non-redundant dataset was performed to evaluate the performance of our model. To alleviate the problem caused by the noise of negative dataset, 300 experiments utilizing 300 sub-datasets were performed. We achieved overall sensitivity of 81.8%, precision of 64.1% and area under the receiver operating characteristic curve (AUC) of 0.728.Conclusions
We have presented a reliable method for the identification of linear B cell epitope using antigen’s primary sequence information. Moreover, a web server EPMLR has been developed for linear B-cell epitope prediction: http://www.bioinfo.tsinghua.edu.cn/epitope/EPMLR/.Electronic supplementary material
The online version of this article (doi:10.1186/s12859-014-0414-y) contains supplementary material, which is available to authorized users. 相似文献18.
Tom Baden Andre Maia Chagas Greg Gage Timothy Marzullo Lucia L. Prieto-Godino Thomas Euler 《PLoS biology》2015,13(3)
The introduction of affordable, consumer-oriented 3-D printers is a milestone in the current “maker movement,” which has been heralded as the next industrial revolution. Combined with free and open sharing of detailed design blueprints and accessible development tools, rapid prototypes of complex products can now be assembled in one’s own garage—a game-changer reminiscent of the early days of personal computing. At the same time, 3-D printing has also allowed the scientific and engineering community to build the “little things” that help a lab get up and running much faster and easier than ever before.Applications of 3-D printing technologies (Fig. 1A, Box 1) have become as diverse as the types of materials that can be used for printing. Replacement parts at the International Space Station may be printed in orbit from durable plastics or metals, while back on Earth the food industry is starting to explore the same basic technology to fold strings of chocolate into custom-shaped confectionary. Also, consumer-oriented laser-cutting technology makes it very easy to cut raw materials such as sheets of plywood, acrylic, or aluminum into complex shapes within seconds. The range of possibilities comes to light when those mechanical parts are combined with off-the-shelf electronics, low-cost microcontrollers like Arduino boards [1], and single-board computers such as a Beagleboard [2] or a Raspberry Pi [3]. After an initial investment of typically less than a thousand dollars (e.g., to set-up a 3-D printer), the only other materials needed to build virtually anything include a few hundred grams of plastic (approximately US$30/kg), cables, and basic electronic components [4,5].Open in a separate windowFig 1Examples of open 3-D printed laboratory tools.
A
1, Components for laboratory tools, such as the base for a micromanipulator [18] shown here, can be rapidly prototyped using 3-D printing. A
2, The printed parts can be easily combined with an off-the-shelf continuous rotation servo-motor (bottom) to motorize the main axis. B
1, A 3-D printable micropipette [8], designed in OpenSCAD [19], shown in full (left) and cross-section (right). B
2, The pipette consists of the printed parts (blue), two biro fillings with the spring, an off-the-shelf piece of tubing to fit the tip, and one screw used as a spacer. B
3, Assembly is complete with a laboratory glove or balloon spanned between the two main printed parts and sealed with tape to create an airtight bottom chamber continuous with the pipette tip. Accuracy is ±2–10 μl depending on printer precision, and total capacity of the system is easily adjusted using two variables listed in the source code, or accessed via the “Customizer” plugin on the thingiverse link [8]. See also the first table.Area Project Source Microscopy Smartphone Microscope
http://www.instructables.com/id/10-Smartphone-to-digital-microscope-conversion
iPad Microscope
http://www.thingiverse.com/thing:31632
Raspberry Pi Microscope
http://www.thingiverse.com/thing:385308
Foldscope
http://www.foldscope.com/
Molecular Biology Thermocycler (PCR)
http://openpcr.org/
Water bath
http://blog.labfab.cc/?p=47
Centrifuge
http://www.thingiverse.com/thing:151406
Dremelfuge
http://www.thingiverse.com/thing:1483
Colorometer
http://www.thingiverse.com/thing:73910
Micropipette
http://www.thingiverse.com/thing:255519
Gel Comb
http://www.thingiverse.com/thing:352873
Hot Plate
http://www.instructables.com/id/Programmable-Temperature-Controller-Hot-Plate/
Magnetic Stirrer
http://www.instructables.com/id/How-to-Build-a-Magnetic-Stirrer/
Electrophysiology Waveform Generator
http://www.instructables.com/id/Arduino-Waveform-Generator/
Open EEG
https://www.olimex.com/Products/EEG/OpenEEG/
Mobile ECG
http://mobilecg.hu/
Extracellular amplifier
https://backyardbrains.com/products/spikerBox
Micromanipulator
http://www.thingiverse.com/thing:239105
Open Ephys
http://open-ephys.org/
Other Syringe pump
http://www.thingiverse.com/thing:210756
Translational Stage
http://www.thingiverse.com/thing:144838
Vacuum pump
http://www.instructables.com/id/The-simplest-vacuum-pump-in-the-world/
Skinner Box
http://www.kscottz.com/open-skinner-box-pycon-2014/