Editing Comparative genomics (section)

==Tools==

Computational tools for analyzing sequences and complete genomes are developing quickly due to the availability of large amount of genomic data. At the same time, comparative analysis tools are progressed and improved. In the challenges about these analyses, it is very important to visualize the comparative results.<ref name="Humana Press">{{cite book |veditors=Bergman NH |title=Comparative Genomics: Volumes 1 and 2 |location=Totowa, New Jersey |publisher=Humana Press |year=2007 |url=https://www.ncbi.nlm.nih.gov/books/NBK1732/ |isbn=978-193411-537-4 |pmid=21250292 |vauthors=Bergman NH}}</ref>

Visualization of sequence conservation is a tough task of comparative sequence analysis. As we know, it is highly inefficient to examine the alignment of long genomic regions manually. Internet-based genome browsers provide many useful tools for investigating genomic sequences due to integrating all sequence-based biological information on genomic regions. When we extract large amount of relevant biological data, they can be very easy to use and less time-consuming.<ref name="Humana Press"/>
* '''[https://genome.ucsc.edu/ UCSC Browser]''': This site contains the reference sequence and working draft assemblies for a large collection of genomes.<ref>{{cite web|title=UCSC Browser|url=http://genome.ucsc.edu/}}</ref>
* '''[[Ensembl genome database project|Ensembl]]''': The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.<ref>{{cite web|title=Ensembl Genome Browser|url=http://asia.ensembl.org/index.html|archive-url=https://archive.today/20131021101058/http://asia.ensembl.org/index.html|url-status=dead|archive-date=2013-10-21}}</ref>
* '''MapView''': The Map Viewer provides a wide variety of genome mapping and sequencing data.<ref>{{cite web|title=Map Viewer|url=https://www.ncbi.nlm.nih.gov/mapview/}}</ref>
* '''[[VISTA (comparative genomics)|VISTA]]''' is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. It was built to visualize the results of comparative analysis based on DNA alignments. The presentation of comparative data generated by VISTA can easily suit both small and large scale of data.<ref>{{cite web|title=VISTA tools|url=http://genome.lbl.gov/vista/index.shtml}}</ref>
* '''BlueJay Genome Browser''': A stand-alone visualization tool for the multi-scale viewing of annotated genomes and other genomic elements.<ref>{{cite journal |vauthors=Soh J, Gordon PM, Sensen CW |title=The Bluejay genome browser |journal=Current Protocols in Bioinformatics |at=Chapter 10, Unit 10.9 |date=March 2012 |volume=37 |pmid=22389011 |doi=10.1002/0471250953.bi1009s37 |publisher=John Wiley & Sons, Inc. |isbn=9780471250951 |s2cid=34553139}}</ref>
* '''[https://schneebergerlab.github.io/syri/ SyRI]:''' SyRI stands for Synteny and Rearrangement Identifier and is a versatile tool for comparative genomics, offering functionalities for synteny analysis and visualization, aiding in the prediction of genomic differences between related genomes using whole-genome assemblies (WGA).<ref>{{cite journal | vauthors = Goel M, Sun H, Jiao WB, Schneeberger K | title = SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies | journal = Genome Biology | volume = 20 | issue = 1 | pages = 277 | date = December 2019 | pmid = 31842948 | pmc = 6913012 | doi = 10.1186/s13059-019-1911-0 | doi-access = free }}</ref>
* '''[https://genomevolution.org/wiki/index.php/SynMap2 Synmap2]:''' Specifically designed for synteny mapping, Synmap2 efficiently compares genetic maps or assemblies, providing insights into genome evolution and rearrangements among related organisms.<ref>{{cite journal | vauthors = Haug-Baltzell A, Stephens SA, Davey S, Scheidegger CE, Lyons E | title = SynMap2 and SynMap3D: web-based whole-genome synteny browsers | journal = Bioinformatics | volume = 33 | issue = 14 | pages = 2197–2198 | date = July 2017 | pmid = 28334338 | doi = 10.1093/bioinformatics/btx144 }}</ref>
* '''[https://github.com/hsinnan75/GSAlign GSAlign]:''' GSAlign facilitates accurate alignment of genomic sequences, particularly useful for large-scale comparative genomics studies, enabling researchers to identify similarities and differences across genomes.<ref>{{cite journal | vauthors = Lin HN, Hsu WL | title = GSAlign: an efficient sequence alignment tool for intra-species genomes | journal = BMC Genomics | volume = 21 | issue = 1 | pages = 182 | date = February 2020 | pmid = 32093618 | pmc = 7041101 | doi = 10.1186/s12864-020-6569-1 | doi-access = free }}</ref>
* '''[https://igv.org/ IGV (Integrative Genomics Viewer)]:''' A widely-used tool for visualizing and analyzing genomic data, IGV supports comparative genomics by enabling users to explore alignments, variants, and annotations across multiple genomes.<ref>{{cite journal | vauthors = Thorvaldsdóttir H, Robinson JT, Mesirov JP | title = Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration | journal = Briefings in Bioinformatics | volume = 14 | issue = 2 | pages = 178–192 | date = March 2013 | pmid = 22517427 | pmc = 3603213 | doi = 10.1093/bib/bbs017 }}</ref>
* '''[https://github.com/Illumina/manta Manta]:''' Manta is a rapid structural variant caller, crucial for comparative genomics as it detects genomic rearrangements such as insertions, deletions, inversions, and duplications, aiding in understanding genetic variation among populations or species.<ref>{{cite journal | vauthors = Chen X, Schulz-Trieglaff O, Shaw R, Barnes B, Schlesinger F, Källberg M, Cox AJ, Kruglyak S, Saunders CT | title = Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications | journal = Bioinformatics | volume = 32 | issue = 8 | pages = 1220–1222 | date = April 2016 | pmid = 26647377 | doi = 10.1093/bioinformatics/btv710 }}</ref>
* '''[https://bioinformaticstools.mayo.edu/research/cnvnator/ CNVNatar]:''' CNVNatar specializes in detecting copy number variations (CNVs), which are crucial in understanding genome evolution and population genetics, providing insights into genomic structural changes across different organisms.<ref>{{cite journal | vauthors = Abyzov A, Urban AE, Snyder M, Gerstein M | title = CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing | journal = Genome Research | volume = 21 | issue = 6 | pages = 974–984 | date = June 2011 | pmid = 21324876 | pmc = 3106330 | doi = 10.1101/gr.114876.110 }}</ref>
* '''[http://pipmaker.bx.psu.edu/pipmaker/ PIPMaker]:''' PIPMaker facilitates the alignment and comparison of two genomic sequences, enabling the identification of conserved regions, duplications, and evolutionary breakpoints, aiding in comparative genomics analyses.<ref>{{cite journal | vauthors = Elnitski L, Riemer C, Schwartz S, Hardison R, Miller W | title = PipMaker: a World Wide Web server for genomic sequence alignments | journal = Current Protocols in Bioinformatics | at=Chapter 10, Unit 10.2 | date = February 2003 | volume = Chapter 10 | pmid = 18428692 | doi = 10.1002/0471250953.bi1002s00 }}</ref>
* '''[https://cb.csail.mit.edu/cb/glass/ GLASS (Genome-wide Location and Sequence Searcher)]:''' GLASS is a tool for identifying conserved regulatory elements across genomes, crucial for comparative genomics studies focusing on understanding gene regulation and evolution.<ref>{{cite journal | vauthors = Pal K, Bystry V, Reigl T, Demko M, Krejci A, Touloumenidou T, Stalika E, Tichy B, Ghia P, Stamatopoulos K, Pospisilova S, Malcikova J, Darzentas N | title = GLASS: assisted and standardized assessment of gene variations from Sanger sequence trace data | journal = Bioinformatics | volume = 33 | issue = 23 | pages = 3802–3804 | date = December 2017 | pmid = 29036643 | doi = 10.1093/bioinformatics/btx423 }}</ref>
* '''[[PatternHunter]]''': PatternHunter is a versatile tool for sequence analysis, offering functionalities for identifying conserved patterns, motifs, and repeats across genomic sequences, aiding in comparative genomics studies of gene families and regulatory elements.
* '''[https://github.com/mummer4/mummer Mummer]:''' Mummer is a suite of tools for whole-genome alignment and comparison, widely used in comparative genomics for identifying similarities, differences, and evolutionary events among genomes at various scales.<ref>{{cite journal | vauthors = Marçais G, Delcher AL, Phillippy AM, Coston R, Salzberg SL, Zimin A | title = MUMmer4: A fast and versatile genome alignment system | journal = PLOS Computational Biology | volume = 14 | issue = 1 | pages = e1005944 | date = January 2018 | pmid = 29373581 | pmc = 5802927 | doi = 10.1371/journal.pcbi.1005944 | doi-access = free | bibcode = 2018PLSCB..14E5944M }}</ref>

An advantage of using online tools is that these websites are being developed and updated constantly. There are many new settings and content can be used online to improve efficiency.<ref name="Humana Press"/>