Evolutionary Bioinformatics Online最新文献_第7页

Segmenting the Human Genome into Isochores 将人类基因组分割成同工

Evolutionary Bioinformatics Online Pub Date : 2015-01-01 DOI: 10.4137/EBO.S27693

P. Cozzi, L. Milanesi, G. Bernardi

引用次数: 24

Screening of Transcription Factors Involved in Fetal Hemoglobin Regulation Using Phylogenetic Footprinting 利用系统发育足迹筛选参与胎儿血红蛋白调节的转录因子

Evolutionary Bioinformatics Online Pub Date : 2015-01-01 DOI: 10.4137/EBO.S15364

Gisele Cristine de Souza Carrocini, L. Venâncio, C. Bonini-Domingos

{"title":"Screening of Transcription Factors Involved in Fetal Hemoglobin Regulation Using Phylogenetic Footprinting","authors":"Gisele Cristine de Souza Carrocini, L. Venâncio, C. Bonini-Domingos","doi":"10.4137/EBO.S15364","DOIUrl":"https://doi.org/10.4137/EBO.S15364","url":null,"abstract":"Fetal hemoglobin (Hb F) is an important genetic modulator of the beta-hemoglobinopathies. The regulation of Hb F levels is influenced by transcription factors. We used phylogenetic footprinting to screen transcription factors that have binding sites in HBG1 and HBG2 genes’ noncoding regions in order to know the genetic determinants of the Hb F expression. Our analysis showed 354 conserved motifs in the noncoding regions of HBG1 gene and 231 motifs in the HBG2 gene between the analyzed species. Of these motifs, 13 showed relation to Hb F regulation: cell division cycle-5 (CDC5), myeloblastosis viral oncogene homolog (c-MYB), transcription factor CP2 (TFCP2), GATA binding protein 1 (GATA-1), GATA binding protein 2 (GATA-2), nuclear factor erythroid 2 (NF-E2), nuclear transcription factor Y (NF-Y), runt-related transcription factor 1 (RUNX-1), T-cell acute lymphocytic leukemia 1 (TAL-1), YY1 transcription factor (YY1), beta protein 1 (BP1), chicken ovalbumin upstream promoter-transcription factor II (COUP-TFII), and paired box 1 (PAX-1). The last three motifs were conserved only in the noncoding regions of the HBG1 gene. The understanding of genetic elements involved in the maintenance of high Hb F levels may provide new efficient therapeutic strategies in the beta-hemoglobinopathies treatment, promoting reduction in clinical complications of these genetic disorders.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126839260","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry 为什么序列特征预测酶的机制?同源性与化学

Evolutionary Bioinformatics Online Pub Date : 2015-01-01 DOI: 10.4137/EBO.S31482

Kirsten E. Beattie, Luna De Ferrari, John B. O. Mitchell

{"title":"Why do Sequence Signatures Predict Enzyme Mechanism? Homology versus Chemistry","authors":"Kirsten E. Beattie, Luna De Ferrari, John B. O. Mitchell","doi":"10.4137/EBO.S31482","DOIUrl":"https://doi.org/10.4137/EBO.S31482","url":null,"abstract":"First, we identify InterPro sequence signatures representing evolutionary relatedness and, second, signatures identifying specific chemical machinery. Thus, we predict the chemical mechanisms of enzyme-catalyzed reactions from catalytic and non-catalytic subsets of InterPro signatures. We first scanned our 249 sequences using InterProScan and then used the MACiE database to identify those amino acid residues that are important for catalysis. The sequences were mutated in silico to replace these catalytic residues with glycine and then again scanned using InterProScan. Those signature matches from the original scan that disappeared on mutation were called catalytic. Mechanism was predicted using all signatures, only the 78 “catalytic” signatures, or only the 519 “non-catalytic” signatures. The non-catalytic signatures gave indistinguishable results from those for the whole feature set, with precision of 0.991 and sensitivity of 0.970. The catalytic signatures alone gave less impressive predictivity, with precision and sensitivity of 0.791 and 0.735, respectively. These results show that our successful prediction of enzyme mechanism is mostly by homology rather than by identifying catalytic machinery.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"11 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"131036646","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

TIRfinder: A Web Tool for Mining Class II Transposons Carrying Terminal Inverted Repeats TIRfinder:一个用于挖掘携带末端反向重复序列的II类转座子的网络工具

Evolutionary Bioinformatics Online Pub Date : 2013-01-01 DOI: 10.4137/EBO.S10619

T. Gambin, M. Startek, K. Walczak, Jarosław Paszek, D. Grzebelus, A. Gambin

{"title":"TIRfinder: A Web Tool for Mining Class II Transposons Carrying Terminal Inverted Repeats","authors":"T. Gambin, M. Startek, K. Walczak, Jarosław Paszek, D. Grzebelus, A. Gambin","doi":"10.4137/EBO.S10619","DOIUrl":"https://doi.org/10.4137/EBO.S10619","url":null,"abstract":"Transposable elements (TEs) can be found in virtually all known genomes; plant genomes are exceptionally rich in this kind of dispersed repetitive sequences. Current knowledge on TE proliferation dynamics places them among the main forces of molecular evolution. Therefore efficient tools to analyze TE distribution in genomes are needed that would allow for comparative genomics studies and for studying TE dynamics in a genome. This was our main motivation underpinning TIRfinder construction–-an efficient tool for mining class II TEs carrying terminal inverted repeats. TIRfinder takes as an input a genomic sequence and information on structural properties of a TE family, and identifies all TEs in the genome showing the desired structural characteristics. The efficiency and small memory requirements of our approach stem from the use of suffix trees to identify all DNA segments surrounded by user-specified terminal inverse repeats (TIR) and target site duplications (TSD) which together constitute a mask. On the other hand, the flexibility of the notion of the TIR/TSD mask makes it possible to use the tool for de novo detection. The main advantages of TIRfinder are its speed, accuracy and convenience of use for biologists. A web-based interface is freely available at http:/bioputer.mimuw.edu.pl/tirfindertool/.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"47 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130715145","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

TreeCmp: Comparison of Trees in Polynomial Time 树在多项式时间内的比较

Evolutionary Bioinformatics Online Pub Date : 2012-01-01 DOI: 10.4137/EBO.S9657

D. Bogdanowicz, K. Giaro, B. Wróbel

引用次数: 102

PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny 一种通过基因组比较挖掘系统发育标记的工具:狐猴(小狐猴属)系统发育的应用

Evolutionary Bioinformatics Online Pub Date : 2012-01-01 DOI: 10.4137/EBO.S9886

R. Lei, Thaine W. Rowley, Lifeng Zhu, Carolyn A. Bailey, Shannon E. Engberg, M. L. Wood, M. Christman, G. Perry, E. Louis, G. Lu

{"title":"PhyloMarker—A Tool for Mining Phylogenetic Markers Through Genome Comparison: Application of the Mouse Lemur (Genus Microcebus) Phylogeny","authors":"R. Lei, Thaine W. Rowley, Lifeng Zhu, Carolyn A. Bailey, Shannon E. Engberg, M. L. Wood, M. Christman, G. Perry, E. Louis, G. Lu","doi":"10.4137/EBO.S9886","DOIUrl":"https://doi.org/10.4137/EBO.S9886","url":null,"abstract":"Molecular phylogeny is a fundamental tool to understanding the evolution of all life forms. One common issue faced by molecular phylogeny is the lack of sufficient molecular markers. Here, we present PhyloMarker, a phylogenomic tool designed to find nuclear gene markers for the inference of phylogeny through multiple genome comparison. Around 800 candidate markers were identified by PhyloMarker through comparison of partial genomes of Microcebus and Otolemur. In experimental tests of 20 randomly selected markers, nine markers were successfully amplified by PCR and directly sequenced in all 17 nominal Microcebus species. Phylogenetic analyses of the sequence data obtained for 17 taxa and nine markers confirmed the distinct lineage inferred from previous mtDNA data. PhyloMarker has also been used by other projects including the herons (Ardeidae, Aves) phylogeny and the Wood mice (Muridae, Mammalia) phylogeny. All source code and sample data are made available at http://bioinfo-srv1.awh.unomaha.edu/phylomarker/.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"15 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"126045486","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 8

easyPAC: A Tool for Fast Prediction, Testing and Reference Mapping of Degenerate PCR Primers from Alignments or Consensus Sequences easyPAC:一个快速预测，测试和参考定位的工具，从序列或一致序列退化PCR引物

Evolutionary Bioinformatics Online Pub Date : 2012-01-01 DOI: 10.4137/EBO.S8870

David Rosenkranz

引用次数: 5

MiIP: The Monomer Identification and Isolation Program MiIP:单体鉴定和分离程序

Evolutionary Bioinformatics Online Pub Date : 2012-01-01 DOI: 10.4137/EBO.S9248

Christopher Bun, William Ziccardi, J. Doering, C. Putonti

引用次数: 2

PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences plutof -一个基于Web的生态和分类学研究工作台，具有真菌ITS序列的在线实现

Evolutionary Bioinformatics Online Pub Date : 2010-01-01 DOI: 10.4137/EBO.S6271

K. Abarenkov, L. Tedersoo, R. Nilsson, K. Vellak, I. Saar, Vilmar Veldre, É. Parmasto, M. Prous, Anne Aan, Margus Ots, O. Kurina, I. Ostonen, J. Jõgeva, Siim Halapuu, K. Põldmaa, M. Toots, J. Truu, K. Larsson, U. Kõljalg

{"title":"PlutoF—a Web Based Workbench for Ecological and Taxonomic Research, with an Online Implementation for Fungal ITS Sequences","authors":"K. Abarenkov, L. Tedersoo, R. Nilsson, K. Vellak, I. Saar, Vilmar Veldre, É. Parmasto, M. Prous, Anne Aan, Margus Ots, O. Kurina, I. Ostonen, J. Jõgeva, Siim Halapuu, K. Põldmaa, M. Toots, J. Truu, K. Larsson, U. Kõljalg","doi":"10.4137/EBO.S6271","DOIUrl":"https://doi.org/10.4137/EBO.S6271","url":null,"abstract":"DNA sequences accumulating in the International Nucleotide Sequence Databases (INSD) form a rich source of information for taxonomic and ecological meta-analyses. However, these databases include many erroneous entries, and the data itself is poorly annotated with metadata, making it difficult to target and extract entries of interest with any degree of precision. Here we describe the web-based workbench PlutoF, which is designed to bridge the gap between the needs of contemporary research in biology and the existing software resources and databases. Built on a relational database, PlutoF allows remote-access rapid submission, retrieval, and analysis of study, specimen, and sequence data in INSD as well as for private datasets though web-based thin clients. In contrast to INSD, PlutoF supports internationally standardized terminology to allow very specific annotation and linking of interacting specimens and species. The sequence analysis module is optimized for identification and analysis of environmental ITS sequences of fungi, but it can be modified to operate on any genetic marker and group of organisms. The workbench is available at http://plutof.ut.ee.","PeriodicalId":136690,"journal":{"name":"Evolutionary Bioinformatics Online","volume":"38 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2010-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125397426","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 248

Evolution of the Influenza A Virus: Some New Advances 甲型流感病毒的进化:一些新进展

Evolutionary Bioinformatics Online Pub Date : 2008-01-30 DOI: 10.4137/EBO.S328

R. Rabadán, H. Robins

引用次数: 16