GenomeComp statistics

Tool stats & trends

Looking to identify usage trends or leading experts?

Protocols

GenomeComp specifications

Information


Unique identifier OMICS_23309
Name GenomeComp
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data Two whole genome sequences.
Input format FASTA, GenBank, EMBL
Operating system Unix/Linux, Mac OS, Windows
Programming languages Perl
Computer skills Medium
Stability No
Maintained No

Versioning


No version available

Publication for GenomeComp

GenomeComp citations

 (7)
library_books

Evidence of recent interspecies horizontal gene transfer regarding nucleopolyhedrovirus infection of Spodoptera frugiperda

2015
BMC Genomics
PMCID: 4861128
PMID: 26607569
DOI: 10.1186/s12864-015-2218-5

[…] e 0.1), penalty for a nucleotide mismatch = −2 (−q −2), reward for a nucleotide match = 1 (−r 1) and filter query sequence = false (−F F). Output files for each genome comparison were drawn using the GenomeComp v1.2 software []. A color code was used for showing different ranges of nucleotide identity. Baculoviridae phylogeny was inferred using the 37 core genes in silico translated from 75 baculo […]

library_books

Specialized adaptation of a lactic acid bacterium to the milk environment: the comparative genomics of Streptococcus thermophilus LMD 9

2011
Microb Cell Fact
PMCID: 3231929
PMID: 21995282
DOI: 10.1186/1475-2859-10-S1-S22

[…] and plasmid maps were constructed using the Microbial Genome Viewer [] and Clone Manager Professional software (Sci-Ed Software, Cary, NC), respectively.Whole genome sequences were aligned using the GenomeComp software tool [] with the external MEGABLAST nucleotide sequence alignment search program available from NCBI (ftp://ftp.ncbi.nih.gov/blast/) and default run parameters. Metabolic pathway m […]

call_split

Recent dermatophyte divergence revealed by comparative and phylogenetic analysis of mitochondrial genomes

2009
BMC Genomics
PMCID: 2693141
PMID: 19457268
DOI: 10.1186/1471-2164-10-238
call_split See protocol

[…] Genomic comparisons of dermatophyte mtDNAs employed GenomeComp []. Orthologs between the mitochondrial genomes of T. rubrum and C. albicans were identified by bidirectional BLASTP comparisons. Fourteen of the 15 conserved proteins (excluding Rps5) were […]

library_books

Chromosomal Rearrangements between Serotype A and D Strains in Cryptococcus neoformans

2009
PLoS One
PMCID: 2677675
PMID: 19436753
DOI: 10.1371/journal.pone.0005524

[…] than 85%. These two criteria were used to ensure stringency, identify robust blast hits, and reduce background noise. These selected blast results were then used as input files and imported into the GenomeComp program to obtain graphic representations of the blast hits, following the program's instructions. In these graphic representations, colored lines connect homologous regions, and the lines […]

library_books

Computational Biology Methods and Their Application to the Comparative Genomics of Endocellular Symbiotic Bacteria of Insects

2009
PMCID: 3055744
PMID: 19495914
DOI: 10.1007/s12575-009-9004-1

[…] epresentations, other programs such as GRAST mark the hits between the two genomes and represent them in a circular way []. Finally, other programs such as ACGT [], GOAL from BROP [], BugView [], and GenomeComp [] have contributed to the field of comparative genomics by linearly representing rearrangements or syntenic information by linking homologous regions between the compared genomes using lin […]

call_split

Complete genome sequence of Shigella flexneri 5b and comparison with Shigella flexneri 2a

2006
BMC Genomics
PMCID: 1550401
PMID: 16822325
DOI: 10.1186/1471-2164-7-173
call_split See protocol

[…] h a frameshift of insertion has altered more than 20% of the amino acid sequence were classed as pseudogenes. Mobile elements and repetitive sequences were identified using the IS FINDER database []. GenomeComp was used for genomic comparison with default parameters []. The comparison figures used in Figure and were exported from GenomeComp with a 1500 bp filter setting along with the scale sett […]

Citations

Looking to check out a full list of citations?

GenomeComp institution(s)
Laboratory of Bioinformatics, Institute of Biophysics, CAS, Chaoyang District, Beijing, China; Chinese National Human Genome Center, Beijing, China; State Key Laboratory for Molecular Virology and Genetic Engineering, Beijing, China
GenomeComp funding source(s)
Supported by the Chinese Academy of Sciences Grant No. KSCX2- 2-07.

GenomeComp reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review GenomeComp