analysis of the genome

Information used to predict genes includes signals in the sequence, content statistics and similarity to known genes. As noted by Attwood (Science, 290, 2000), there are many obstacles to accurate gene counting. First there is the problem of what exactly constitutes a gene. Is it a heritable unit corresponding to an observable phenotype? Is it a packet of genetic information that encodes an RNA or a protein? Must it be translated? Answeres to these question affect estimates of the total number of genes in sequenced genomes.

Cross-References: Protein Bioinformatics DNA/RNA Bioinformatics

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DNA Databases BLAST Genbank at NCBI EMBL DNA DDBJ

http://www.ncbi.nlm.nih.gov/LocusLink/” style=”color: rgb(146, 172, 186); -webkit-transition: background-color 0.2s ease-in-out, color 0.2s ease-in-out; transition: background-color 0.2s ease-in-out, color 0.2s ease-in-out;”>LocusLink (NCBI)

Annotation on genes: MedMiner

Analysis of complete genomes: PEDANT

Cloning/Enzymes: BRENDA SwissProt Restriction Enzyme Database Cloneit DNA artist download

Cut your DNA Sequence: NEB Cutter Web Cutter

Vector contamination: EMBL EBI NCBI VecScreen

Mammalian Gene Collection: Mammalian Gene Collection (MGI) (cDNA sequences for human, rat & mouse)

enes involved in Human Disease: GeneCards OMIN

Open Reading Frames (OPFs): ORF Finder ORF Finder (NCBI) Expasy-translate Sequence Manip Site

Comparison of genomes: Institute for Genomic Research TIGR Vista PipMaker

Sequence Submission: GenBank Submissions (BankIt) NCBI GenBank Examples NCBI Sequin (This is software developed by NCBI which must be downloaded. Use this for sequences which are too short to submit online with BankIt or where you want more control over your submissions) Sequin Help Sequin Facts http://www.ebi.ac.uk/embl/Submission/webin.html” style=”color: rgb(146, 172, 186); -webkit-transition: background-color 0.2s ease-in-out, color 0.2s ease-in-out; transition: background-color 0.2s ease-in-out, color 0.2s ease-in-out;”>EMBL (WebIn)

Sequence Analysis: Metagene

Sequence Conversion: (Convert sequence files from one particular format to another format)

ReadSeq Readseqimple ReadseqBaylor Readseqfinice Readseqbioportal readseqebi Redseqbimas

Specific genomes: FlyBase newsnetwork

Wiring Diagrams of life: KEGG