This help document describes the mouse, rat, rodent, or human sequence databases you can select from the MouseBLAST query form when searching for sequences that may be associated with mouse genes.

• Nucleotide Sequence Databases
• Protein Sequence Databases
• Using MouseBLAST - Overview

Nucleotide Sequence Databases

• GenBank Mouse - Subset of GenBank containing mouse sequences from rodent, high-throughput cDNAs (HTC), and patent divisions. Mouse sequences are parsed from these divisions by examining the phylogeny lines for entries containing "mus." Does not include ESTs, genome survey sequences (GSS), and high-throughput genomic sequences (HTGS).


• GenBank GSS Mouse - Subset of GenBank containing mouse genome survey sequences (GSS). All mouse sequences are parsed from the GSS division by examining the phylogeny lines for those entries containing "mus."


• GenBank Human - Subset of GenBank containing human sequences from primate, high-throughput cDNAs (HTC), and patent divisions. Human sequences are parsed from these divisions by examining the phylogeny lines for entries containing "sapiens." Does not include ESTs, genome survey sequences (GSS), and high-throughput genomic sequences (HTGS).


• GenBank Rodent - Subset of GenBank containing rodent sequences from rodent, high-throughput cDNAs (HTC), and patent divisions. Rodent sequences are parsed from these divisions by examining the phylogeny lines for entries containing "rodentia." Does not include ESTs, genome survey sequences (GSS), and high-throughput genomic sequences (HTGS).


• RefSeq Mouse Transcripts - All NCBI RefSeq Mouse transcripts (Mouse RefSeqs of type NM_, NR_, XM_, and XR_).

Protein Sequence Databases

• UniProt Mouse - All mouse protein sequences from the "non-redundant" set of sequences from SwissProt and TrEMBL (SP_TR_NRDB from SIB/EBI). Mouse sequences are defined as those entries containing "mus" in the phylogeny lines or "mouse" in the species lines.


• UniProt Human - All human protein sequences from the "non-redundant" set of sequences from SwissProt and TrEMBL (SP_TR_NRDB from SIB/EBI). Human sequences are defined as those entries containing "sapiens" in the phylogeny lines or "human" in the species lines.


• UniProt Rat - All rat protein sequences from the "non-redundant" set of sequences from SwissProt and TrEMBL (SP_TR_NRDB from SIB/EBI). Rat sequences are defined as those entries containing "rattus" in the phylogeny lines or "rat" in the species lines.