What are UniGene clusters?

UniGene is an experimental system for automatically partitioning GenBank sequences into a non-redundant set of gene-oriented clusters. Each UniGene cluster contains sequences that represent a unique gene, as well as related information such as the tissue types in which the gene has been expressed and map location.

How many human clusters are in UniGene?

Together, a total of 59,500 UNIGENE clusters have been mapped, providing an early glimpse of a complete transcript map for the human genome….Table 1.

	Known genes	Anonymous ESTs
UNIGENE clusters	11191	75,925
Singletons	692	29,689
UNIGENE clusters extended	7237	22,795
Average number of transcripts	97	18

What is the use of UniGene database in NCBI Entrez?

UniGene has since been used as a source of approximate expression profiles, an index of available cDNA clones, and as a guide to transcript-oriented resource design.

What is EST database?

dbEST (Nature Genetics 4:332-3;1993) is a division of GenBank that contains sequence data and other information on “single-pass” cDNA sequences, or “Expressed Sequence Tags”, from a number of organisms. A brief account of the history of human ESTs in GenBank is available (Trends Biochem.

What is UniGene ID?

Query terms can be, for example, the UniGene identifier, a gene name, a text term that is found somewhere in the UniGene record, or the accession number of an EST or gene sequence in the cluster.

What is TrEMBL?

Introduction TrEMBL is a computer-annotated protein sequence database supplementing the SWISS-PROT Protein Sequence Data Bank. TrEMBL contains the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database not yet integrated in SWISS-PROT.

What is Insdc and what does it stand for?

The International Nucleotide Sequence Database Collaboration (INSDC) is a long-standing foundational initiative that operates between DDBJ, EMBL-EBI and NCBI.

What is EST marker?

In genetics, an expressed sequence tag (EST) is a short sub-sequence of a cDNA sequence. ESTs may be used to identify gene transcripts, and were instrumental in gene discovery and in gene-sequence determination.

What are the uses of EST?

EST sequences contain at least partial sequences of most mRNAs present in the various tissues used for library construction. Therefore, they have been used intensively as a source of information for the discovery of new genes whose function can be tentatively deduced from their sequence, and experimentally verified.

What is a contig in sequencing?

A contig (as related to genomic studies; derived from the word “contiguous”) is a set of DNA segments or sequences that overlap in a way that provides a contiguous representation of a genomic region.

What is UniRef50?

UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.

What does UniProt stand for?

The Universal Protein Resource
The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc).

What does DDBJ stand for?

The DNA Data Bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) (1) is a public database of nucleotide sequences established at the National Institute of Genetics (NIG).

What is EST SSR?

Expressed sequence tag-derived simple sequence repeat markers (EST-SSRs) are the markers of choice, because they are abundant, co-dominant, highly polymorphic, and are easily transferable among phylogenetically related species [13].

What is SAGE technique?

SAGE technique works by isolating short fragments of genetic information from the expressed genes that are present in the cell under study. These unique sequence tags (9–10 base pairs in length) are concatenated serially into long DNA molecules for lump-sum sequencing [3].

How are ESTs generated?

ESTs are generated by sequencing cDNA, which itself is synthesized from the mRNA molecules in a cell. The mRNA in a cell are copies of the genes that are being expressed.

What is the purpose of a contig?

Definition. A contig (as related to genomic studies; derived from the word “contiguous”) is a set of DNA segments or sequences that overlap in a way that provides a contiguous representation of a genomic region.

What is a contig and scaffold?

A scaffold is a portion of the genome sequence reconstructed from end-sequenced whole-genome shotgun clones. Scaffolds are composed of contigs and gaps. A contig is a contiguous length of genomic sequence in which the order of bases is known to a high confidence level.

What is UniRef100?

The UniRef100 database combines identical sequences and subfragments from any source organism into a single UniRef entry (i.e. cluster). UniRef90 and UniRef50 are built by clustering UniRef100 sequences at the 90% or 50% sequence identity levels.

What is the difference between UniProt and Swiss-Prot?

Protein families and groups of proteins are continuously reviewed to keep up with current scientific findings. UniProtKB/TrEMBL is a computer-annotated (unreviewed) supplement to Swiss-Prot, which strives to gather all protein sequences that are not yet represented in Swiss-Prot.

What is UniGene and how does it work?

You are correct; UniGene is a database and not a biological concept. It contains all of the RNA molecules produced by a cell. This is a pretty cool database since RNA production is not static. Thank you all for the answers.

What is the average length of a UniGene?

The average length of a unigene was 956 bp. We detected 12,139 SNPs and indel loci using BWA software and Samtools software, which included 8681 SNPs. After filtering out low quality data according to the criteria of FDR ≤0.001 and |log 2 Ratio| ≥ 1, we obtained 7368 SNPs and indel loci, which included 4436 SNPs.

What makes a sequence a candidate for entry into UniGene?

After a sequence is screened, it must contain at least 100 bases to be a candidate for entry into UniGene. mRNA and genomic DNA are clustered first into gene links. A second sequence comparison links ESTs to each other and to the gene links.

What are query terms in Unigene?

Query terms can be, for example, the UniGene identifier, a gene name, a text term that is found somewhere in the UniGene record, or the accession number of an EST or gene sequence in the cluster.