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52 result(s) for 'Tblastx' within BMC Bioinformatics

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  1. Phylogenetic methods which do not rely on multiple sequence alignments are important tools in inferring trees directly from completely sequenced genomes. Here, we extend the recently described Genome BLAST Distan...

    Authors: Alexander F Auch, Stefan R Henz, Barbara R Holland and Markus Göker
    Citation: BMC Bioinformatics 2006 7:350
    Content type: Research article Published on:

  2. Serial Analysis of Gene Expression (SAGE) is a method of large-scale gene expression analysis that has the potential to generate the full list of mRNAs present within a cell population at a given time and thei...

    Authors: Céline Keime, Francesca Damiola, Dominique Mouchiroud, Laurent Duret and Olivier Gandrillon
    Citation: BMC Bioinformatics 2004 5:143
    Content type: Software Published on:

  3. The decreasing costs of capillary-based Sanger sequencing and next generation technologies, such as 454 pyrosequencing, have prompted an explosion of transcriptome projects in non-model species, where even sha...

    Authors: Alexie Papanicolaou, Remo Stierli, Richard H ffrench-Constant and David G Heckel
    Citation: BMC Bioinformatics 2009 10:447
    Content type: Software Published on:

  4. In recent years, many studies focused on the description and comparison of large sets of related bacteriophage genomes. Due to the peculiar mosaic structure of these genomes, few informative approaches for com...

    Authors: Sèverine Bérard, Annie Chateau, Nicolas Pompidor, Paul Guertin, Anne Bergeron and Krister M. Swenson
    Citation: BMC Bioinformatics 2016 17:30
    Content type: Methodology Article Published on:

  5. The inference of splicing orthology relationships between gene transcripts is a basic step for the prediction of transcripts and the annotation of gene structures in genomes. The splicing structure of a sequen...

    Authors: Safa Jammali, Jean-David Aguilar, Esaie Kuitche and Aïda Ouangraoua
    Citation: BMC Bioinformatics 2019 20(Suppl 3):133
    Content type: Research Published on:

    This article is part of a Supplement: Volume 20 Supplement 3

  6. Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which ...

    Authors: Eduardo Eyras, Alexandre Reymond, Robert Castelo, Jacqueline M Bye, Francisco Camara, Paul Flicek, Elizabeth J Huckle, Genis Parra, David D Shteynberg, Carine Wyss, Jane Rogers, Stylianos E Antonarakis, Ewan Birney, Roderic Guigo and Michael R Brent
    Citation: BMC Bioinformatics 2005 6:131
    Content type: Research article Published on:

  9. BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), whi...

    Authors: Scot E Dowd, Joaquin Zaragoza, Javier R Rodriguez, Melvin J Oliver and Paxton R Payton
    Citation: BMC Bioinformatics 2005 6:93
    Content type: Software Published on:

  10. The Lepidoptera Spodoptera frugiperda is a pest which causes widespread economic damage on a variety of crop plants. It is also well known through its famous Sf9 cell line which is used for numerous heterologous ...

    Authors: Vincent Nègre, Thierry Hôtelier, Anne-Nathalie Volkoff, Sylvie Gimenez, François Cousserans, Kazuei Mita, Xavier Sabau, Janick Rocher, Miguel López-Ferber, Emmanuelle d'Alençon, Pascaline Audant, Cécile Sabourault, Vincent Bidegainberry, Frédérique Hilliou and Philippe Fournier
    Citation: BMC Bioinformatics 2006 7:322
    Content type: Database Published on:

  12. Several small open reading frames located within the 5′ untranslated regions of mRNAs have recently been shown to be translated. In humans, about 50% of mRNAs contain at least one upstream open reading frame r...

    Authors: Adam Skarshewski, Mitchell Stanton-Cook, Thomas Huber, Sumaya Al Mansoori, Ross Smith, Scott A Beatson and Joseph A Rothnagel
    Citation: BMC Bioinformatics 2014 15:36
    Content type: Software Published on:

  13. Sequence similarity searching is a very important bioinformatics task. While Basic Local Alignment Search Tool (BLAST) outperforms exact methods through its use of heuristics, the speed of the current BLAST so...

    Authors: Christiam Camacho, George Coulouris, Vahram Avagyan, Ning Ma, Jason Papadopoulos, Kevin Bealer and Thomas L Madden
    Citation: BMC Bioinformatics 2009 10:421
    Content type: Software Published on:

  14. Large molecular sequence databases are fundamental resources for modern bioscientists. Whether for project-specific purposes or sharing data with colleagues, it is often advantageous to maintain smaller sequen...

    Authors: Scott A Givan, Christopher M Sullivan and James C Carrington
    Citation: BMC Bioinformatics 2007 8:479
    Content type: Software Published on:

  15. Repbase is a reference database of eukaryotic repetitive DNA, which includes prototypic sequences of repeats and basic information described in annotations. Updating and maintenance of the database requires sp...

    Authors: Oleksiy Kohany, Andrew J Gentles, Lukasz Hankus and Jerzy Jurka
    Citation: BMC Bioinformatics 2006 7:474
    Content type: Software Published on:

  16. Single-pass, partial sequencing of complementary DNA (cDNA) libraries generates thousands of chromatograms that are processed into high quality expressed sequence tags (ESTs), and then assembled into contigs r...

    Authors: Charu G Kumar, Richard LeDuc, George Gong, Levan Roinishivili, Harris A Lewin and Lei Liu
    Citation: BMC Bioinformatics 2004 5:176
    Content type: Software Published on:

  17. Metagenomics, based on culture-independent sequencing, is a well-fitted approach to provide insights into the composition, structure and dynamics of environmental viral communities. Following recent advances i...

    Authors: Simon Roux, Jeremy Tournayre, Antoine Mahul, Didier Debroas and François Enault
    Citation: BMC Bioinformatics 2014 15:76
    Content type: Software Published on:

  18. Detecting duplication segments within completely sequenced genomes provides valuable information to address genome evolution and in particular the important question of the emergence of novel functions. The us...

    Authors: Eric Audemard, Thomas Schiex and Thomas Faraut
    Citation: BMC Bioinformatics 2012 13:83
    Content type: Methodology article Published on:

  20. In the past decade, transcriptome data have become an important component of many phylogenetic studies. They are a cost-effective source of protein-coding gene sequences, and have helped projects grow from a f...

    Authors: Casey W Dunn, Mark Howison and Felipe Zapata
    Citation: BMC Bioinformatics 2013 14:330
    Content type: Software Published on:

  21. Gene prediction is one of the most important steps in the genome annotation process. A large number of software tools and pipelines developed by various computing techniques are available for gene prediction. ...

    Authors: Kuang-Lim Chan, Rozana Rosli, Tatiana V. Tatarinova, Michael Hogan, Mohd Firdaus-Raih and Eng-Ti Leslie Low
    Citation: BMC Bioinformatics 2017 18(Suppl 1):1426
    Content type: Research Published on:

    This article is part of a Supplement: Volume 18 Supplement 1

  22. wFleaBase is a database with the necessary infrastructure to curate, archive and share genetic, molecular and functional genomic data and protocols for an emerging model organism, the microcrustacean Daphnia. Com...

    Authors: John K Colbourne, Vasanth R Singan and Don G Gilbert
    Citation: BMC Bioinformatics 2005 6:45
    Content type: Database Published on:

  26. Legumes (Leguminosae or Fabaceae) play a major role in agriculture. Transcriptomics studies in the model legume species, Medicago truncatula, are instrumental in helping to formulate hypotheses about the role of ...

    Authors: Ji He, Vagner A Benedito, Mingyi Wang, Jeremy D Murray, Patrick X Zhao, Yuhong Tang and Michael K Udvardi
    Citation: BMC Bioinformatics 2009 10:441
    Content type: Database Published on:

  27. Sequencing of EST and BAC end datasets is no longer limited to large research groups. Drops in per-base pricing have made high throughput sequencing accessible to individual investigators. However, there are f...

    Authors: Stephen E Diener, Thomas D Houfek, Sam E Kalat, DE Windham, Mark Burke, Charles Opperman and Ralph A Dean
    Citation: BMC Bioinformatics 2005 6:147
    Content type: Software Published on:

  29. Non-coding RNA (ncRNA) genes do not encode proteins but produce functional RNA molecules that play crucial roles in many key biological processes. Recent genome-wide transcriptional profiling studies using til...

    Authors: Dandan Song, Yang Yang, Bin Yu, Binglian Zheng, Zhidong Deng, Bao-Liang Lu, Xuemei Chen and Tao Jiang
    Citation: BMC Bioinformatics 2009 10(Suppl 1):S36
    Content type: Research Published on:

    This article is part of a Supplement: Volume 10 Supplement 1

  31. Biologists are faced with an ever-changing array of complex software tools with steep learning curves, often run on High Performance Computing platforms. To resolve the tradeoff between analytical sophisticati...

    Authors: Graham Alvare, Abiel Roche-Lima and Brian Fristensky
    Citation: BMC Bioinformatics 2023 24:316
    Content type: Software Published on:

  33. Graph-based representation of genome assemblies has been recently used in different contexts — from improved reconstruction of plasmid sequences and refined analysis of metagenomic data to read error correctio...

    Authors: Tatiana Dvorkina, Dmitry Antipov, Anton Korobeynikov and Sergey Nurk
    Citation: BMC Bioinformatics 2020 21(Suppl 12):306
    Content type: Software Published on:

    This article is part of a Supplement: Volume 21 Supplement 12

  34. In order to improve gene prediction, extrinsic evidence on the gene structure can be collected from various sources of information such as genome-genome comparisons and EST and protein alignments. However, suc...

    Authors: Mario Stanke, Oliver Schöffmann, Burkhard Morgenstern and Stephan Waack
    Citation: BMC Bioinformatics 2006 7:62
    Content type: Research article Published on:

  37. Automated gene-calling is still an error-prone process, particularly for the highly plastic genomes of fungal species. Improvement through quality control and manual curation of gene models is a time-consuming...

    Authors: Ate van der Burgt, Edouard Severing, Jérôme Collemare and Pierre JGM de Wit
    Citation: BMC Bioinformatics 2014 15:19
    Content type: Methodology article Published on:

  38. Transposable elements (TEs) are mobile sequences found in nearly all eukaryotic genomes. They have the ability to move and replicate within a genome, often influencing genome evolution and gene expression. The...

    Authors: Ryan C Kennedy, Maria F Unger, Scott Christley, Frank H Collins and Gregory R Madey
    Citation: BMC Bioinformatics 2011 12:130
    Content type: Methodology article Published on:

  39. We present Pegasys – a flexible, modular and customizable software system that facilitates the execution and data integration from heterogeneous biological sequence analysis tools.

    Authors: Sohrab P Shah, David YM He, Jessica N Sawkins, Jeffrey C Druce, Gerald Quon, Drew Lett, Grace XY Zheng, Tao Xu and BF Francis Ouellette
    Citation: BMC Bioinformatics 2004 5:40
    Content type: Software Published on:

  40. An important initial phase of arguably most homology search and alignment methods such as required for genome alignments is seed finding. The seed finding step is crucial to curb the runtime as potential alignmen...

    Authors: Matthis Ebel, Giovanna Migliorelli and Mario Stanke
    Citation: BMC Bioinformatics 2022 23:225
    Content type: Research article Published on:

  41. Due to recent advances in whole genome shotgun sequencing and assembly technologies, the financial cost of decoding an organism's DNA has been drastically reduced, resulting in a recent explosion of genomic se...

    Authors: Todd J Treangen and Xavier Messeguer
    Citation: BMC Bioinformatics 2006 7:433
    Content type: Software Published on:

  42. Multivariate approaches have been successfully applied to genome wide association studies. Recently, a Partial Least Squares (PLS) based approach was introduced for mapping yeast genotype-phenotype relations, ...

    Authors: Tahir Mehmood, Jonas Warringer, Lars Snipen and Solve Sæbø
    Citation: BMC Bioinformatics 2012 13:327
    Content type: Research article Published on:

  43. Spliced Leader trans-splicing is an important mechanism for the maturation of mRNAs in several lineages of eukaryotes, including several groups of parasites of great medical and economic importance. Neverthele...

    Authors: Javier Calvelo, Hernán Juan, Héctor Musto, Uriel Koziol and Andrés Iriarte
    Citation: BMC Bioinformatics 2020 21:293
    Content type: Software Published on:

  44. Analysis of any newly sequenced bacterial genome starts with the identification of protein-coding genes. Despite the accumulation of multiple complete genome sequences, which provide useful comparisons with cl...

    Authors: Stéphanie Bocs, Antoine Danchin and Claudine Médigue
    Citation: BMC Bioinformatics 2002 3:5
    Content type: Research article Published on:

  46. Many potentially life-threatening infectious viruses are highly mutable in nature. Characterizing the fittest variants within a quasispecies from infected patients is expected to allow unprecedented opportunit...

    Authors: Wan-Ting Poh, Eryu Xia, Kwanrutai Chin-inmanu, Lai-Ping Wong, Anthony Youzhi Cheng, Prida Malasit, Prapat Suriyaphol, Yik-Ying Teo and Rick Twee-Hee Ong
    Citation: BMC Bioinformatics 2013 14:355
    Content type: Methodology article Published on:

  48. Multivariate approaches are important due to their versatility and applications in many fields as it provides decisive advantages over univariate analysis in many ways. Genome wide association studies are rapi...

    Authors: Tahir Mehmood, Harald Martens, Solve Sæbø, Jonas Warringer and Lars Snipen
    Citation: BMC Bioinformatics 2011 12:318
    Content type: Research article Published on:

  50. “Omics” approaches may provide useful information for a deeper understanding of speciation events, diversification and function innovation. This can be achieved by investigating the molecular similarities at s...

    Authors: Luca Ambrosino, Valentino Ruggieri, Hamed Bostan, Marco Miralto, Nicola Vitulo, Mohamed Zouine, Amalia Barone, Mondher Bouzayen, Luigi Frusciante, Mario Pezzotti, Giorgio Valle and Maria Luisa Chiusano
    Citation: BMC Bioinformatics 2018 19(Suppl 15):435
    Content type: Research Published on:

    This article is part of a Supplement: Volume 19 Supplement 15

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