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Zabel S, Müller J, Götz F, Nieselt K. BLASTphylo: An Interactive Web Tool for Taxonomic and Phylogenetic Analysis of Prokaryotic Genes. J Comput Biol 2023; 30:999-1008. [PMID: 37624644 DOI: 10.1089/cmb.2023.0156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/27/2023] Open
Abstract
Identifying a protein's function is crucial to reveal its role in the cellular complex. Computationally, the most common approach is to search for homologous proteins in a large database of proteins of known function using BLAST. One goal of such an analysis is the identification and visualization of the protein in the taxonomy of interest. Another goal is the reconstruction of the phylogenetic history of the protein. However, the BLAST result provides information about the occurrence of the protein in the taxonomy and its putative function mainly in a tabular format. This requires manual interventions and makes the taxonomic identification laborious. Although various tools exist to visualize and annotate large-scale trees, none of them intuitively and interactively visualizes the protein's occurrence in the taxonomy for different taxonomic ranks. To target this gap, we developed BLASTphylo, a web tool that combines BLAST with automatic taxonomic mapping and phylogenetic analysis and provides the results in interactive visualizations. We demonstrate the functionalities of BLASTphylo in two case studies.
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Affiliation(s)
- Susanne Zabel
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
| | | | - Friedrich Götz
- Institute for Microbiology and Infection-Medicine, University of Tübingen, Tübingen, Germany
| | - Kay Nieselt
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany
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2
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BuscoPhylo: a webserver for Busco-based phylogenomic analysis for non-specialists. Sci Rep 2022; 12:17352. [PMID: 36253435 PMCID: PMC9576783 DOI: 10.1038/s41598-022-22461-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/14/2022] [Indexed: 01/10/2023] Open
Abstract
Here we present the BuscoPhylo tool that enables both students and established scientists to easily perform Busco-based phylogenomic analysis starting from a set of genomes sequences. BuscoPhylo is an efficient and user-friendly web server freely accessible at https://buscophylo.inra.org.ma/ . The source code, along with documentation, is freely available under an MIT license at https://github.com/alaesahbou/BuscoPhylo .
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3
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Kuraku S, Zmasek CM, Nishimura O, Katoh K. aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity. Nucleic Acids Res 2013; 41:W22-8. [PMID: 23677614 PMCID: PMC3692103 DOI: 10.1093/nar/gkt389] [Citation(s) in RCA: 401] [Impact Index Per Article: 36.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
We report a new web server, aLeaves (http://aleaves.cdb.riken.jp/), for homologue collection from diverse animal genomes. In molecular comparative studies involving multiple species, orthology identification is the basis on which most subsequent biological analyses rely. It can be achieved most accurately by explicit phylogenetic inference. More and more species are subjected to large-scale sequencing, but the resultant resources are scattered in independent project-based, and multi-species, but separate, web sites. This complicates data access and is becoming a serious barrier to the comprehensiveness of molecular phylogenetic analysis. aLeaves, launched to overcome this difficulty, collects sequences similar to an input query sequence from various data sources. The collected sequences can be passed on to the MAFFT sequence alignment server (http://mafft.cbrc.jp/alignment/server/), which has been significantly improved in interactivity. This update enables to switch between (i) sequence selection using the Archaeopteryx tree viewer, (ii) multiple sequence alignment and (iii) tree inference. This can be performed as a loop until one reaches a sensible data set, which minimizes redundancy for better visibility and handling in phylogenetic inference while covering relevant taxa. The work flow achieved by the seamless link between aLeaves and MAFFT provides a convenient online platform to address various questions in zoology and evolutionary biology.
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Affiliation(s)
- Shigehiro Kuraku
- Genome Resource and Analysis Unit, RIKEN Center for Developmental Biology, Kobe, Hyogo 650-0047, Japan.
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4
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Woo SG, Srinivasan S, Kim MK, Lee M. Rhodanobacter caeni sp. nov., isolated from sludge from a sewage disposal plant. Int J Syst Evol Microbiol 2012; 62:2815-2821. [DOI: 10.1099/ijs.0.033365-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Two Gram-reaction-negative, motile bacteria, designated strains MJ01T and MJ14, were isolated from sludge collected from the Daejeon sewage disposal plant in South Korea. The taxonomic positions of both strains were determined using a polyphasic approach. In phylogenetic analyses based on 16S rRNA gene sequences, strains MJ01T and MJ14 appeared indistinguishable and to be most closely related to members of the genus
Rhodanobacter
in the family
Xanthomonadaceae
of the
Gammaproteobacteria
(96.4–98.8 % sequence similarity). Strain MJ01T exhibited a relatively high level of DNA–DNA relatedness with strain MJ14 (89.3 %) but relatively low DNA–DNA relatedness values with established species in the genus
Rhodanobacter
(<60 %). The genomic DNA G+C contents of strains MJ01T and MJ14 were 65.3 and 64.8 mol%, respectively. The major respiratory quinone of both novel strains was the ubiquinone Q-8. The major fatty acids of both strains were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and iso-C17 : 1ω9c, and the polar lipid profiles of the two strains contained diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and minor amounts of unidentified aminophospholipids and phospholipids. Based on the phenotypic, genotypic and phylogenetic evidence, strains MJ01T and MJ14 represent a single novel species in the genus
Rhodanobacter
, for which the name Rhodanobacter caeni sp. nov. is proposed. The type strain is MJ01T ( = KCTC 22449T = JCM 16242T), with MJ14 ( = KCTC 22460 = JCM 16243) as a reference strain.
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Affiliation(s)
- Sung-Geun Woo
- School of Civil and Environmental Engineering, Yonsei University, Seoul 120-749, Republic of Korea
- Research and Development Division, H-Plus Eco Ltd, BVC #301, KRIBB, Eoeun-dong, Yuseong-gu, Daejeon 305-333, Republic of Korea
| | - Sathiyaraj Srinivasan
- Department of Bio and Environmental Technology, Division of Environmental and Life Science, College of Natural Science, Seoul Women’s University, 623 Hwarangno, Nowon-gu, Seoul 139-774, Republic of Korea
- Research and Development Division, H-Plus Eco Ltd, BVC #301, KRIBB, Eoeun-dong, Yuseong-gu, Daejeon 305-333, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio and Environmental Technology, Division of Environmental and Life Science, College of Natural Science, Seoul Women’s University, 623 Hwarangno, Nowon-gu, Seoul 139-774, Republic of Korea
| | - Myungjin Lee
- Research and Development Division, H-Plus Eco Ltd, BVC #301, KRIBB, Eoeun-dong, Yuseong-gu, Daejeon 305-333, Republic of Korea
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5
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Srinivasan S, Park G, Yang H, Hwang S, Bae Y, Jung YA, Kim MK, Lee M. Gordonia caeni sp. nov., isolated from sludge of a sewage disposal plant. Int J Syst Evol Microbiol 2012; 62:2703-2709. [DOI: 10.1099/ijs.0.029736-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A Gram-stain-positive, strictly aerobic, short-rod-shaped, non-motile strain (designated MJ32T) was isolated from a sludge sample of the Daejeon sewage disposal plant in South Korea. A polyphasic approach was applied to study the taxonomic position of strain MJ32T. Strain MJ32T showed highest 16S rRNA gene sequence similarity to
Gordonia hirsuta
DSM 44140T (98.1 %) and
Gordonia hydrophobica
DSM 44015T (97.0 %); levels of sequence similarity to the type strains of other recognized
Gordonia
species were less than 97.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ32T belonged to the clade formed by members of the genus
Gordonia
in the family
Gordoniaceae
. The G+C content of the genomic DNA of strain MJ32T was 69.2 mol%. Chemotaxonomically, strain MJ32T showed features typical of the genus
Gordonia
. The predominant respiratory quinone was MK-9(H2), the mycolic acids present had C56–C60 carbon atoms, and the major fatty acids were C16 : 0 (34.6 %), tuberculostearic acid (21.8 %), C16 : 1ω7c (19.5 %) and C18 : 1ω9c (12.7 %). The peptidoglycan type was based on meso-2,6-diaminopimelic acid as the diagnostic diamino acid with glycolated sugars. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ32T is considered to represent a novel species of the genus
Gordonia
, for which the name Gordonia caeni sp. nov. is proposed. The type strain is MJ32T ( = KCTC 19771T = JCM 16923T).
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Affiliation(s)
- Sathiyaraj Srinivasan
- Research and Development Division, H-Plus Eco Ltd, BVC no. 301, KRIBB, Eoeun-dong, Yuseong-gu, Daejeon, 305-333, Republic of Korea
- Department of Bio & Environmental Technology, Division of Environmental & Life Science, College of Natural Science, Seoul Women’s University, 623 Hwarangno, Nowon-gu, Seoul 139-774, Republic of Korea
| | - Giho Park
- Daewoo Institute of Construction Technology, 60 Songjuk-dong, Jangan-gu, Suwon-si, Gyeonggi-do 440-210, Republic of Korea
| | - Hyejin Yang
- Department of Bio & Environmental Technology, Division of Environmental & Life Science, College of Natural Science, Seoul Women’s University, 623 Hwarangno, Nowon-gu, Seoul 139-774, Republic of Korea
| | - Supyong Hwang
- Department of Bio & Environmental Technology, Division of Environmental & Life Science, College of Natural Science, Seoul Women’s University, 623 Hwarangno, Nowon-gu, Seoul 139-774, Republic of Korea
| | - Yoonjung Bae
- Department of Bio & Environmental Technology, Division of Environmental & Life Science, College of Natural Science, Seoul Women’s University, 623 Hwarangno, Nowon-gu, Seoul 139-774, Republic of Korea
| | - Yong-An Jung
- Korea Testing Certification, Chemical Industry Team, 587-10, Sinsa-Dong, Gangnam-Gu, Seoul, Republic of Korea
| | - Myung Kyum Kim
- Department of Bio & Environmental Technology, Division of Environmental & Life Science, College of Natural Science, Seoul Women’s University, 623 Hwarangno, Nowon-gu, Seoul 139-774, Republic of Korea
| | - Myungjin Lee
- Daewoo Institute of Construction Technology, 60 Songjuk-dong, Jangan-gu, Suwon-si, Gyeonggi-do 440-210, Republic of Korea
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Nocardioides daejeonensis sp. nov., a denitrifying bacterium isolated from sludge in a sewage-disposal plant. Int J Syst Evol Microbiol 2012; 62:1199-1203. [DOI: 10.1099/ijs.0.033308-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Strain MJ31T, a Gram-reaction-positive, aerobic, rod-shaped, non-motile bacterium, was isolated from a sludge sample collected at the Daejeon sewage-disposal plant, in South Korea, and characterized in order to determine its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain MJ31T belonged to the genus
Nocardioides
, appearing most closely related to
Nocardioides dubius
KSL-104T (98.6 % sequence similarity),
Nocardioides jensenii
DSM 20641T (97.6 %),
Nocardioides daedukensis
MDN22T (97.2 %) and
Nocardioides mesophilus
MSL-22T (97.0 %). The chemotaxonomic properties of strain MJ31T were consistent with those of the genus
Nocardioides
: MK-8(H4) was the predominant menaquinone, iso-C16 : 0, iso-C17 : 0 and C18 : 1ω9c were the predominant cellular fatty acids, and the cell-wall peptidoglycan was based on ll-2,6-diaminopimelic acid. The genomic DNA G+C content of strain MJ31T was 71.2 mol%. Some differential phenotypic properties and low DNA–DNA relatedness values (<28 %) with the type strains of closely related species indicated that strain MJ31T represents a novel species, for which the name Nocardioides daejeonensis sp. nov. is proposed. The type strain is MJ31T ( = KCTC 19772T = JCM 16922T).
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Kim HJ, Lee SS. Leucobacter kyeonggiensis sp. nov., a new species isolated from dye waste water. J Microbiol 2011; 49:1044-9. [DOI: 10.1007/s12275-011-1548-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 12/08/2011] [Indexed: 11/29/2022]
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8
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Lee M, Srinivasan S, Kim MK. New taxa in Alphaproteobacteria: Brevundimonas olei sp. nov., an esterase-producing bacterium. J Microbiol 2010; 48:616-22. [DOI: 10.1007/s12275-010-9367-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2009] [Accepted: 05/26/2010] [Indexed: 10/18/2022]
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Stenotrophomonas panacihumi sp. nov., isolated from soil of a ginseng field. J Microbiol 2010; 48:30-5. [DOI: 10.1007/s12275-010-0006-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2010] [Accepted: 02/17/2010] [Indexed: 10/19/2022]
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Dereeper A, Audic S, Claverie JM, Blanc G. BLAST-EXPLORER helps you building datasets for phylogenetic analysis. BMC Evol Biol 2010; 10:8. [PMID: 20067610 PMCID: PMC2821324 DOI: 10.1186/1471-2148-10-8] [Citation(s) in RCA: 496] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2009] [Accepted: 01/12/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The right sampling of homologous sequences for phylogenetic or molecular evolution analyses is a crucial step, the quality of which can have a significant impact on the final interpretation of the study. There is no single way for constructing datasets suitable for phylogenetic analysis, because this task intimately depends on the scientific question we want to address, Moreover, database mining softwares such as BLAST which are routinely used for searching homologous sequences are not specifically optimized for this task. RESULTS To fill this gap, we designed BLAST-Explorer, an original and friendly web-based application that combines a BLAST search with a suite of tools that allows interactive, phylogenetic-oriented exploration of the BLAST results and flexible selection of homologous sequences among the BLAST hits. Once the selection of the BLAST hits is done using BLAST-Explorer, the corresponding sequence can be imported locally for external analysis or passed to the phylogenetic tree reconstruction pipelines available on the Phylogeny.fr platform. CONCLUSIONS BLAST-Explorer provides a simple, intuitive and interactive graphical representation of the BLAST results and allows selection and retrieving of the BLAST hit sequences based a wide range of criterions. Although BLAST-Explorer primarily aims at helping the construction of sequence datasets for further phylogenetic study, it can also be used as a standard BLAST server with enriched output. BLAST-Explorer is available at http://www.phylogeny.fr.
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Affiliation(s)
- Alexis Dereeper
- Information Génomique & Structurale-CNRS-UPR2589, Institut de Microbiologie de la Méditerranée-IFR 88, Marseille, France
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11
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Han Y, Burnette JM, Wessler SR. TARGeT: a web-based pipeline for retrieving and characterizing gene and transposable element families from genomic sequences. Nucleic Acids Res 2009; 37:e78. [PMID: 19429695 PMCID: PMC2699529 DOI: 10.1093/nar/gkp295] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2009] [Revised: 04/15/2009] [Accepted: 04/15/2009] [Indexed: 11/23/2022] Open
Abstract
Gene families compose a large proportion of eukaryotic genomes. The rapidly expanding genomic sequence database provides a good opportunity to study gene family evolution and function. However, most gene family identification programs are restricted to searching protein databases where data are often lagging behind the genomic sequence data. Here, we report a user-friendly web-based pipeline, named TARGeT (Tree Analysis of Related Genes and Transposons), which uses either a DNA or amino acid 'seed' query to: (i) automatically identify and retrieve gene family homologs from a genomic database, (ii) characterize gene structure and (iii) perform phylogenetic analysis. Due to its high speed, TARGeT is also able to characterize very large gene families, including transposable elements (TEs). We evaluated TARGeT using well-annotated datasets, including the ascorbate peroxidase gene family of rice, maize and sorghum and several TE families in rice. In all cases, TARGeT rapidly recapitulated the known homologs and predicted new ones. We also demonstrated that TARGeT outperforms similar pipelines and has functionality that is not offered elsewhere.
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Affiliation(s)
| | | | - Susan R. Wessler
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA
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12
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Dereeper A, Guignon V, Blanc G, Audic S, Buffet S, Chevenet F, Dufayard JF, Guindon S, Lefort V, Lescot M, Claverie JM, Gascuel O. Phylogeny.fr: robust phylogenetic analysis for the non-specialist. Nucleic Acids Res 2008; 36:W465-9. [PMID: 18424797 PMCID: PMC2447785 DOI: 10.1093/nar/gkn180] [Citation(s) in RCA: 3290] [Impact Index Per Article: 205.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Phylogenetic analyses are central to many research areas in biology and typically involve the identification of homologous sequences, their multiple alignment, the phylogenetic reconstruction and the graphical representation of the inferred tree. The Phylogeny.fr platform transparently chains programs to automatically perform these tasks. It is primarily designed for biologists with no experience in phylogeny, but can also meet the needs of specialists; the first ones will find up-to-date tools chained in a phylogeny pipeline to analyze their data in a simple and robust way, while the specialists will be able to easily build and run sophisticated analyses. Phylogeny.fr offers three main modes. The 'One Click' mode targets non-specialists and provides a ready-to-use pipeline chaining programs with recognized accuracy and speed: MUSCLE for multiple alignment, PhyML for tree building, and TreeDyn for tree rendering. All parameters are set up to suit most studies, and users only have to provide their input sequences to obtain a ready-to-print tree. The 'Advanced' mode uses the same pipeline but allows the parameters of each program to be customized by users. The 'A la Carte' mode offers more flexibility and sophistication, as users can build their own pipeline by selecting and setting up the required steps from a large choice of tools to suit their specific needs. Prior to phylogenetic analysis, users can also collect neighbors of a query sequence by running BLAST on general or specialized databases. A guide tree then helps to select neighbor sequences to be used as input for the phylogeny pipeline. Phylogeny.fr is available at: http://www.phylogeny.fr/
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Affiliation(s)
- A Dereeper
- Information Génomique et Structurale (IGS), CNRS-UPR2589, IFR-88, Marseille, France
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Hanekamp K, Bohnebeck U, Beszteri B, Valentin K. PhyloGena--a user-friendly system for automated phylogenetic annotation of unknown sequences. Bioinformatics 2007; 23:793-801. [PMID: 17332025 DOI: 10.1093/bioinformatics/btm016] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION Phylogenomic approaches towards functional and evolutionary annotation of unknown sequences have been suggested to be superior to those based only on pairwise local alignments. User-friendly software tools making the advantages of phylogenetic annotation available for the ever widening range of bioinformatically uninitiated biologists involved in genome/EST annotation projects are, however, not available. We were particularly confronted with this issue in the annotation of sequences from different groups of complex algae originating from secondary endosymbioses, where the identification of the phylogenetic origin of genes is often more problematic than in taxa well represented in the databases (e.g. animals, plants or fungi). RESULTS We present a flexible pipeline with a user-friendly, interactive graphical user interface running on desktop computers that automatically performs a basic local alignment search tool (BLAST) search of query sequences, selects a representative subset of them, then creates a multiple alignment from the selected sequences, and finally computes a phylogenetic tree. The pipeline, named PhyloGena, uses public domain software for all standard bioinformatics tasks (similarity search, multiple alignment, and phylogenetic reconstruction). As the major technological innovation, selection of a meaningful subset of BLAST hits was implemented using logic programming, mimicing the selection procedure (BLAST tables, multiple alignments and phylogenetic trees) are displayed graphically, allowing the user to interact with the pipeline and deduce the function and phylogenetic origin of the query. PhyloGena thus makes phylogenomic annotation available also for those biologists without access to large computing facilities and with little informatics background. Although phylogenetic annotation is particularly useful when working with composite genomes (e.g. from complex algae), PhyloGena can be helpful in expressed sequence tag and genome annotation also in other organisms. AVAILABILITY PhyloGena (executables for LINUX and Windows 2000/XP as well as source code) is available by anonymous ftp from http://www.awi.de/en/phylogena.
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Affiliation(s)
- Kristian Hanekamp
- Center for Computing Technologies (TZI), P.O.B. 330440, D-28334 Bremen, Germany
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Lin CY, Lin FK, Lin CH, Lai LW, Hsu HJ, Chen SH, Hsiung CA. POWER: PhylOgenetic WEb Repeater--an integrated and user-optimized framework for biomolecular phylogenetic analysis. Nucleic Acids Res 2005; 33:W553-6. [PMID: 15980533 PMCID: PMC1160254 DOI: 10.1093/nar/gki494] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
POWER, the PhylOgenetic WEb Repeater, is a web-based service designed to perform user-friendly pipeline phylogenetic analysis. POWER uses an open-source LAMP structure and infers genetic distances and phylogenetic relationships using well-established algorithms (ClustalW and PHYLIP). POWER incorporates a novel tree builder based on the GD library to generate a high-quality tree topology according to the calculated result. POWER accepts either raw sequences in FASTA format or user-uploaded alignment output files. Through a user-friendly web interface, users can sketch a tree effortlessly in multiple steps. After a tree has been generated, users can freely set and modify parameters, select tree building algorithms, refine sequence alignments or edit the tree topology. All the information related to input sequences and the processing history is logged and downloadable for the user's reference. Furthermore, iterative tree construction can be performed by adding sequences to, or removing them from, a previously submitted job. POWER is accessible at .
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Affiliation(s)
- Chung-Yen Lin
- Division of Biostatistics and Bioinformatics, National Health Research Institutes, 35 Keyan Road, Zhunan Town, Miaoli County 350, Taiwan.
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15
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Abstract
Expressed sequence tag (EST) data are a major contributor to the known plant sequence space. Organization of the data into non-redundant clusters representing tentative unique genes provides snapshots of the gene repertoires of a species. This chapter reviews availability of sequences and sequence analysis results and describes several resources and tools that should facilitate broad-based utilization of EST data for gene structure annotation, gene discovery, and comparative genomics.
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Affiliation(s)
- Qunfeng Dong
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011-3260, USA
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16
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Kalra S, Li N, Yammani RR, Seetharam S, Seetharam B. Cobalamin (vitamin B12) binding, phylogeny, and synteny of human transcobalamin. Arch Biochem Biophys 2004; 431:189-96. [PMID: 15488467 DOI: 10.1016/j.abb.2004.08.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2004] [Revised: 08/09/2004] [Indexed: 10/26/2022]
Abstract
Selected residues in a highly conserved 15-residue region, 174SVDTAAMAGLAFTC L188 of human transcobalamin (TC), a cobalamin (Cbl: vitamin B12) binding protein, were subjected to site-directed mutagenesis. The mutant constructs were expressed in TC-deficient fibroblasts or in vitro to assess the effect of these mutations on Cbl binding. Phylogenetic analyses and protein parsimony indicated that TC evolved earlier than other mammalian Cbl-binding proteins, intrinsic factor and haptocorrins, and divergence occurred between mouse/rat and human dispersing TC gene to different chromosomes. These studies show that (a) two of the three polar residues, S174, T177, or D176 and two of the three conserved alanine residues, A179 and A184 present in the 15-residue evolutionary conserved region are essential for Cbl-binding by human TC, and (b) TC gene is transferred in a syntenic manner to different chromosomes, at least before the divergence of mouse/rat and human.
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Affiliation(s)
- Seema Kalra
- Division of Gastroenterology and Hepatology, Department of Medicine, Medical College of Wisconsin and Clement Zablocki VA Medical Center, Milwaukee, WI 53295, USA
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Gopalaswamy R, Narayanan PR, Narayanan S. Cloning, overexpression, and characterization of a serine/threonine protein kinase pknI from Mycobacterium tuberculosis H37Rv. Protein Expr Purif 2004; 36:82-9. [PMID: 15177288 DOI: 10.1016/j.pep.2004.03.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2004] [Revised: 03/19/2004] [Indexed: 01/29/2023]
Abstract
Protein phosphorylation-dephosphorylation is the principal mechanism for translation of external signals into cellular responses. Eukaryotic-like serine/threonine kinases have been reported to play important roles in bacterial development and/or virulence. The PknI protein is one of the 11 eukaryotic-like serine/threonine kinases in Mycobacterium tuberculosis H37Rv. From the bioinformatic studies, PknI protein has been shown to have an N-terminal cytoplasmic domain followed by a transmembrane region and an extracellular C-terminus suggestive of a sensor molecule. In this study, we have cloned, overexpressed, and characterized the entire coding region and the cytoplasmic domain of PknI as a fusion protein with an N-terminal histidine tag, and used immobilized metal affinity chromatography for purification of recombinant proteins. The purified recombinant proteins were found to be functionally active through in vitro phosphorylation assay and phosphoamino acid analysis. In vitro kinase assay of both proteins revealed that PknI is capable of autophosphorylation and showed manganese-dependent activity. Phosphoamino acid analysis indicated phosphorylation at serine and threonine residues. Southern blot analysis with genomic DNA highlighted the conserved nature of pknI among the various mycobacterial species. In silico analysis revealed a close homology of PknI to Stk1 from Streptococcus agalactiae, shown to have a role in virulence and cell segregation of the organism.
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Affiliation(s)
- Radha Gopalaswamy
- Department of Immunology, Tuberculosis Research Centre (ICMR), Mayor V.R. Ramanathan Road, Chetput, Chennai 600031, India
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2001. [PMCID: PMC2447222 DOI: 10.1002/cfg.60] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
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