• MEGA

  • Referenced in 35 articles [sw09078]
  • application designed for comparative analysis of homologous gene sequences either from multigene families or from...
  • TERA

  • Referenced in 4 articles [sw34318]
  • amalgamated from a sample of gene trees. Using a large scale simulated dataset, we demonstrate ... TERA on a set of 1099 homologous gene families from complete cyanobacterial genomes, we find...
  • FragGeneScan

  • Referenced in 4 articles [sw17159]
  • MetaGene predicted (>90% of the genes identified by homology search), and many novel genes with...
  • BLAT

  • Referenced in 36 articles [sw16891]
  • homologous regions. It stitches together these aligned regions (often exons) into larger alignments (typically genes...
  • QuartetS

  • Referenced in 2 articles [sw34206]
  • events can be used to discriminate homologous genes, QuartetS uses an approximate phylogenetic analysis...
  • Hum-PLoc

  • Referenced in 24 articles [sw26863]
  • unknown query proteins do not have significant homology to proteins of known subcellular locations ... protein samples are expressed by hybridizing the gene ontology (GO) database and amphiphilic pseudo amino ... membrane. To get rid of redundancy and homology bias, none of the proteins investigated here...
  • Euk-PLoc

  • Referenced in 24 articles [sw22420]
  • unknown query proteins do not have significant homology to proteins of known subcellular locations ... hybridizing the information derived from the gene ontology database and amphiphilic pseudo amino acid composition ... body, and (18) vacuole. To avoid the homology bias, none of the proteins included...
  • GOASVM

  • Referenced in 6 articles [sw22445]
  • problem. Recently, several computational methods based on Gene Ontology (GO) have been proposed to tackle ... from the GO term frequencies and distant homologs to represent a protein in the general ... homologs to find the number of occurrences of the selected GO terms in the Gene ... strategy to incorporate useful homologous information, GOASVM can achieve a prediction accuracy...
  • FsePSA

  • Referenced in 0 articles [sw17418]
  • from a same gene or from homologous genes, while accounting for their codon structure ... from homologous emph{human}, emph{mouse} and emph{cow} genes of ten mammalian gene families...
  • eHive

  • Referenced in 2 articles [sw27408]
  • whole genome alignments and (3) gene trees with protein homology inference. Finally, we show...
  • DiagHunter

  • Referenced in 1 article [sw36927]
  • GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization. The DiagHunter and GenoPix2D ... both genome-wide and single-gene scales. DiagHunter identifies homologous regions (synteny blocks) within...
  • AUGUSTUS

  • Referenced in 10 articles [sw10926]
  • AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences ... sequence files and allows to use protein homology information in the prediction. The MediGRID requires...
  • ARAGORN

  • Referenced in 2 articles [sw16999]
  • genes. The program employs heuristic algorithms to predict tRNA secondary structure, based on homology with ... form a base‐paired cloverleaf. tmRNA genes are identified using a modified version...
  • ProCARs

  • Referenced in 1 article [sw29623]
  • Orders. Background: In the context of ancestral gene order reconstruction from extant genomes, there exist ... main computational approaches: rearrangement-based, and homology-based methods. The rearrangement-based methods consist ... this paper, we present a new homology-based method that uses a progressive approach ... boreoeutherian ancestral gene order, and a comparison with three other homology-based methods: AnGeS, InferCARs...
  • MCScanX

  • Referenced in 1 article [sw29671]
  • toolkit for detection and evolutionary analysis of gene synteny and collinearity. MCScan is an algorithm ... identify putative homologous chromosomal regions, and align these regions using genes as anchors. The MCScanX...
  • OrthoDB

  • Referenced in 5 articles [sw22979]
  • free software. Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies ... become instrumental for generating hypotheses about gene functions crucial to many studies. This update...
  • AceView

  • Referenced in 3 articles [sw23000]
  • Gene names when available, else by AceView gene names, stable from release to release. Alternative ... coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression ... sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially...
  • i-ADHoRe

  • Referenced in 1 article [sw29669]
  • unveil genomic homology based on the identification of conservation of gene content and gene order ... more sensitive to detect degenerate genomic homology than chaining pairwise collinearity information based on transitive...
  • Conrad

  • Referenced in 1 article [sw23028]
  • combine standalone gene predictors with additional information such as ESTs and protein homology, Conrad encodes ... inference algorithms. Conrad outperforms the best standalone gene predictors in cross-validation and whole chromosome...
  • GoFigure

  • Referenced in 2 articles [sw35755]
  • have developed a web tool to predict Gene Ontology (GO) terms. The tool accepts ... protein sequence, and uses BLAST to identify homologous sequences in GO annotated databases. A graph...