GOALS IN SIMILARITY SEARCHING

Hypothesis on function

UniGene

Assessment of evolutionary relations

HomoloGene

Synteny groups

UniGene is an organized view of

the transcriptoma

Each entry provides comparison of sequences with reference sequence of a selected protein.

The alignments can suggest function of a gene.

A derivative database that provides sets of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene).

In Genes and Expression

http://www.ncbi.nlm.nih.gov/ unigene

Link rete

Cftr and Homo Sapiens

Unigene Cluster in MapViewer

HOMOLOGY

EVOLUTIONARY RELATION BETWEEN SINGLE GENES

HOMOLOGENE

HomoloGene is a system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.

HOMOLOGENE GROUPS ARE BASED ON HOMOLOGY BETWEEN PROTEINS

SEARCHING FOR CFTR HOMOLOGOUS GROUPS

BLAST ALIGNMENT

PRECOMPUTED PAIRWISE BLAST

SYNTENY

EVOLUTIONARY RELATION

BETWEEN GENOMIC REGIONS

SYNTENY

Chromosome regions containing associated genes (syntenic groups) show conservation in different species.

Ensembl

Ensembl is a joint project between the EBI (European Bioinformatics Institute) and the Wellcome Trust Sanger Institute that annotates chordate genomes (i.e. vertebrates and closely related invertebrates with a notochord).

Ensembl

The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.

available genome information

Human Chromosome 1 Sinteny link

Syntenic group of human

chromosome 1

Syntenic regions are calculated from pairwise (two-species) comparison of the whole genome. The view presents synteny between two species

Species of interest (human)

Syntenic regions in the second species (mouse)

Blocks are coloured and connected by lines. A black line indicates regions with opposite orientation. Brown lines connect syntenic blocks with the same orientation.

Select a chromosomal region; the localization of the corresponding genes is shown in both species

the X chromosome shows synteny only with X chromosome of the mouse and of other mammals.

Genes located in the X chromosome tend to

remain associated in this chromosome during evolution.

In fact genes located on the X chromosome are active in single copy in males and also in females (one x chromosome is inactive).

Syntenic groups (X chromosome)

Sinteny between H.sapiens and mouse

chr. X

Sinteny between H.sapiens and chimpanzee

chr. X

chromosome 2 sinteny of the human and chimpanzee chromosome 2

The chimp has one extra chromosome in respect to Homo sapiens. To try to explain the origin of the extra chimp chromosome, you can view chromosome 2 sinteny and compare the human and chimp chromosomes 2.

chromosome 2 sinteny human and chimpanzee

The human chromosome 2 derives from the fusion of chimp chromosomes 2A and 2B.

Synteny between other human and chimp chromosomes

Looking for synteny between other chromosomes: many syntenic groups in the two species are in the same chromosome.

The closer are the species, the more conserved are the synteny groups and their chromosome localization.

Taxonomy

Is a secondary database

Records are organized on the basis of the taxonomic lineage

Taxonomy database contains the names and lineages of more than 160,000 organisms, both living and extinct, that are represented in NCBI's genetic databases with at least one nucleotide or protein sequence.

Taxonomy Browser is a tool that supports searching the taxonomy tree using partial taxonomic names, common names and phonetically similar names. For each taxonomic node, the tool provides links to all data in Entrez for that node, displays the lineage, and provides links to external sites related to the node.

Links to taxonomic tree

Select how many records are present in each species or sub-species