Homology & Comparisons

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Homology & Comparisons


	Comparisons within S. cerevisiae
	BLAST Search yeast DNA and protein sequence datasets FASTA Search yeast DNA and protein sequence datasets Pairwise Chromosome Similarity View Chromosome by chromosome similarity matrices of yeast chromosomes
	Potential orthologs in other species
	P-POD (Princeton Protein Orthology Database) Groups proteins from the Reference Genomes into families of predicted orthologs or into larger families of more distantly-related homologs and provides functional conservation information curated from the literature. PSI-BLAST Results Displays the results of a sequence analysis in which every protein sequence in S. cerevisiae is used as the query sequence for PSI-BLAST analysis against UniProt's UniRef90 protein dataset Fungal BLAST Search Tool for BLAST searches against all fungal nucleotide or protein sequences in GenBank, using an input sequence provided by the user. Model Organism BLASTP Best Hits Displays the results of NCBI BLASTP analysis using the protein sequence of each S. cerevisiae open reading frame as the query sequence against the predicted protein sequences of several model organisms. Fungal Alignment Viewer Displays ClustalW alignments of S. cerevisiae protein or nucleotide sequences with those of other fungi. The default display shows an alignment of the S. cerevisiae protein sequence with potential orthologs from other fungi; a selection menu allows you to generate custom alignments by choosing the species to include and the type of sequence to align. Synteny Viewer Displays the genome wide alignments among the very closely related S. cerevisiae, S. paradoxus, S. mikatae, and S. bayanus species, based on Kellis et al.
	Structural and Motif Comparisons
	PDB Homolog Query This query page allows you to search for structural information on Saccharomyces cerevisiae proteins; in addition, SGD also provides a protein structure viewer resource page Yeast Protein Domain/Motif Query This query page allows you to retrieve domain/motif information for Saccharomyces cerevisiae proteins Structural assignments of proteins This external site provides structural assignments to protein sequences at the superfamily level. You can browse an overview of all the superfamilies currently identified in S. cerevisiae; the site also provides several different ways to search this information. See Gough et al. for more information.