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Protein family alignment annotation

D. Gilbert
2003 Briefings in Bioinformatics  
This open-source software includes methods for viewing and aligning protein families, and for annotating sequence structure and residues with known functions.  ...  For bioscientists studying protein structure and function, the Protein Family Alignment Annotation Tool (Pfaat) is a useful and simple program for annotating collections of proteins.  ...  It offers a new, needed entry to annotating and viewing information on aligned protein families.  ... 
doi:10.1093/bib/4.2.192 pmid:12846399 fatcat:yhauiphlh5e5rg3io3tpduarea

A Brief Review of Software Tools for Pangenomics

Jingfa Xiao, Zhewen Zhang, Jiayan Wu, Jun Yu
2015 Genomics, Proteomics & Bioinformatics  
The functions of the software packages and tools, albeit variable among them, include categorizing orthologous genes, calculating pangenomic profiles, integrating gene annotations, and constructing phylogenies  ...  genes and non-protein-coding sequences including non-coding RNAs, insertion elements, and conserved structural elements.  ...  In 2014, another rapid core-genome alignment and visualization pangenomic software package, Harvest, was proposed by Treangen et al.  ... 
doi:10.1016/j.gpb.2015.01.007 pmid:25721608 pmcid:PMC4411478 fatcat:k3wmxjhy5jfuzl66gk3xec45am

A Review of Software for Predicting Gene Function

Swee Kuan Loh, Swee Thing Low, Mohd Saberi Mohamad, Safaai Deris, Shahreen Kasim, Choon Yee Wen, Zuwairie Ibrahim, Bambang Susilo, Yusuf Hendrawan, Agustin Krisna Wardani
2015 International Journal of Bio-Science and Bio-Technology  
These methods explore genomic context by major recent advances in the bioinformatics fields rather than by sequence alignment. This paper reviews software related to predicting gene function.  ...  Web links to the software are provided as well.  ...  The phylogenetic trees are estimated using multiple alignments of proteins by the MAFFT alignment program.  ... 
doi:10.14257/ijbsbt.2015.7.2.06 fatcat:nedrong7bzhqrgzqhholgfguyq

REVIEW OF SOFTWARE TOOLS FOR GENETIC MUTATION ANALYSIS

Augustine Chidibere Onuora, Nonye Emmanuel Maidoh, Godwin Oko Epia, Prince Ana, Prince Ana, Prince Ana
2020 International Journal of Engineering Applied Sciences and Technology  
These applications were reviewed stating the OS platform it depends on, the nature and format of data it accept, the input and output from these software tools and urls were they can be found were also  ...  Some genes act as instructions to make molecules called proteins. However, many genes do not code for proteins. Gene Mutation refers to modification of gene's DNA sequence.  ...  Some of these softwares listed above will be reviewed based on data available at OmicX.  ... 
doi:10.33564/ijeast.2020.v05i08.003 fatcat:vc4zjjygm5hd5g6k2t7xfejgtq

GFAP: ultra-fast and accurate gene functional annotation software for plants [article]

Dong Xu, Kangming Jin, Heling Jiang, Desheng Gong, Jinbao Yang, Wenjuan Yu, Yingxue Yang, Jihong Li, Weihua Pan
2022 bioRxiv   pre-print
Here, we collected the protein sequences of 236 plant species with known genomic information from 63 families.  ...  Sequence alignment is the basis of gene functional annotation for unknow sequences.  ...  The alignment process was completed by the diamond software (Hernández-Salmerón and Moreno-Hagelsieb, 2020) to increase the alignment efficiency.  ... 
doi:10.1101/2022.01.05.475154 fatcat:lgmzjqsuyjfvtnmdllqr6vk6va

Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools

Deborah Antunes, Natasha A. N. Jorge, Ernesto R. Caffarena, Fabio Passetti
2018 Frontiers in Genetics  
In this review, we describe software and web servers currently available for riboswitch aptamer identification and secondary and tertiary structure prediction, including applications.  ...  Computational prediction of protein structures is a research field in which high confidence three-dimensional protein models can be proposed based on the sequence alignment between target and templates  ...  First, the software utilizes a set of reliable sequence alignments, along with a common secondary structure annotation (Stockholm format), to create the CM model specific for that target RNA family.  ... 
doi:10.3389/fgene.2017.00231 pmid:29403526 pmcid:PMC5780412 fatcat:kaugkql5mrfzrjo4f5uofphgfu

Common introns within orthologous genes: software and application to plants

M. D. Wilkerson, Y. Ru, V. P. Brendel
2009 Briefings in Bioinformatics  
based on position and sequence conservation in the corresponding protein alignments.  ...  Here, we describe new, freely available software called Common Introns Within Orthologous Genes (CIWOG), available at http://ciwog.gdcb.iastate.edu/, which detects common introns in protein-coding genes  ...  We also thank anonymous reviewers for their thoughtful and useful comments.  ... 
doi:10.1093/bib/bbp051 pmid:19933210 fatcat:tyxdco4nw5hwbpfifmlg2nwevu

WormBase: better software, richer content

E. M. Schwarz
2006 Nucleic Acids Research  
Performance was improved by accelerating the loading of central data pages such as the omnibus Gene page, by rationalizing internal data structures and software for greater portability, and by making the  ...  of protein families (18) , and C.briggsae homologies (5). 5 0 -and 3 0 -UTRs in WormBase are now automatically generated as part of full-length coding transcripts, taking into account additional data  ...  WormBook provides a text companion to WormBase with contributions by >100 expert biologists reviewing and synthesizing the facts presented in WormBase.  ... 
doi:10.1093/nar/gkj061 pmid:16381915 pmcid:PMC1347424 fatcat:t3p5g7dkfbhgrmfm4esppxynse

TransposonUltimate: software for transposon classification, annotation and detection [article]

Kevin Riehl, Cristian Riccio, Eric A. Miska, Martin Hemberg
2021 bioRxiv   pre-print
The annotation and detection modules combine sixteen existing softwares, and we illustrate its use by annotating Caenorhabditis elegans, Rhizophagus irregularis and Oryza sativa subs. japonica genomes.  ...  Finally, we use the detection module to discover 29,554 transposition events in the genomes of twenty wild type strains of Caenorhabditis elegans.AvailabilityRunning software and source code available  ...  Acknowledgements We would like to thank Sarah Buddle, Simone Procaccia, Fu Xiang Quah and Alexandra Dallaire for assistance with testing and debugging the software.  ... 
doi:10.1101/2021.04.30.442214 fatcat:jro4lx2ed5a4blofvzxhrvlhha

KinFin: Software for taxon-aware analysis of clustered protein sequences [article]

Dominik R Laetsch, Mark L Blaxter
2017 bioRxiv   pre-print
We present KinFin, a streamlined software solution capable of integrating data from common file formats and delivering aggregative annotation of protein clusters.  ...  We resolve the phylogenetic relationships between the species and explore functional annotation of proteins in clusters in key lineages and between custom taxon sets, identifying gene families of interest  ...  Resulting text files can easily be interrogated using common UNIX 5 command line tools or spreadsheet software. 6 . CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder.  ... 
doi:10.1101/159145 fatcat:7dtjocxdgjhv5klsp72wdqb7y4

Proteomic databases and software on the web

J. Wojcik
2000 Briefings in Bioinformatics  
maps of protein expression or interaction.  ...  This paper describes the proteomics databases and software available through the World-Wide Web, focusing on their present use and applicability.  ...  Acknowledgements We thank Dr Whiteside and Dr Legrain for their numerous comments on this review.  ... 
doi:10.1093/bib/1.3.250 pmid:11465036 fatcat:vx5mvpwqcjg5foq5vxzfj2mdfi

GLUE: A flexible software system for virus sequence data [article]

Joshua B Singer, Emma C Thomson, John McLauchlan, Joseph Hughes, Robert J Gifford
2018 bioRxiv   pre-print
The GLUE core data schema organises sequence data along evolutionary lines, capturing not only nucleotide data but associated items such as alignments, genotype definitions, genome annotations and motifs  ...  HCV sequence data from GenBank is categorised and stored in a large-scale sequence alignment which is accessible via web-based queries.  ...  Host species objects themselves could then be annotated with ecological factors or associated with host genus or host family objects if these higher-rank taxonomic groups are of interest.  ... 
doi:10.1101/269274 fatcat:fgwenomdtbc2pawsso6evatxuu

Re-purposing software for functional characterization of the microbiome

Laura-Jayne Gardiner, Niina Haiminen, Filippo Utro, Laxmi Parida, Ed Seabolt, Ritesh Krishna, James H. Kaufman
2021 Microbiome  
Background Widespread bioinformatic resource development generates a constantly evolving and abundant landscape of workflows and software.  ...  Instead, we can directly compare sequencing reads to a functionally annotated database.  ...  Although we develop a functional hierarchy and repurpose taxonomic sequence classification software for functional annotation, our GO term reference database can still be used with other alignment software  ... 
doi:10.1186/s40168-020-00971-1 pmid:33422152 fatcat:mni7a5dxo5bmfcgaqdzdydbsy4

Conceptualizing a Genomics Software Institute (GSI)

Jack A. Gilbert, Charlie Catlett, Narayan Desai, Rob Knight, Owen White, Robert Robbins, Rajesh Sankaran, Susanna-Assunta Sansone, Dawn Field, Folker Meyer
2012 Standards in Genomic Sciences  
The majority of the protein-coding genes (59.7%) were assigned a putative function while the remaining ones were annotated as hypothetical proteins.  ...  Additional gene prediction analysis and functional annotation was performed within the Integrated Microbial Genomes -Expert Review (IMG-ER) platform [44] .  ... 
doi:10.4056/sigs.2485911 pmid:22675605 pmcid:PMC3359878 fatcat:ht3u73j3t5hbdendnaqihnuqda

KinFin: Software for Taxon-Aware Analysis of Clustered Protein Sequences

Dominik R. Laetsch, Mark L. Blaxter
2017 G3: Genes, Genomes, Genetics  
We present KinFin, a streamlined software solution capable of integrating data from common file formats and delivering aggregative annotation of protein clusters.  ...  We resolve the phylogenetic relationships between the species and explore functional annotation of proteins in clusters in key lineages and between custom taxon sets, identifying gene families of interest  ...  We thank Duncan Berger for testing the software. D.R.L. is supported by a James Hutton Institute/Edinburgh University School of Biological Sciences fellowship. LITERATURE CITED  ... 
doi:10.1534/g3.117.300233 pmid:28866640 pmcid:PMC5633385 fatcat:qnhscletkbdabof7tyhoc6bkaq
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