ToolSearch

From NMPDR Wiki

The sequence search is designed to locate matching DNA or protein sequences among selected genomes in the NMPDR database. It includes three BLAST tools and two pattern-matching tools, protScan and dnaScan.

The Tool dropdown allows you to select which tool to use for the search. In each case, the genomes to be searched are selected using the Genome Control.

• blastp compares an input protein sequence to the protein databases for the selected genomes.
• blastn compares an input DNA sequence to the nucleotide databases for the selected genomes, which should be closely related to the organism that is the source of the query sequence.
• blastx translates an input DNA sequence and compares all frames to the protein databases for the selected genomes, which may be distantly related to the organism that is the source of the query sequence.
• dnaScan matches a DNA search pattern against the nucleotide databases for the selected genomes.
• protScan matches a protein search pattern against the protein databases for the selected genomes.

For the BLAST tools, enter a DNA sequence, a protein sequence, or a FIG ID for your input, or query, sequence. DNA or protein sequences may be in raw format, listing just the single letter code for the query sequence, or the input may be in FASTA format, which includes a header, as shown below.

>2-amino-4-hydroxy-6-hydroxymethyldihydropteridine pyrophosphokinase
MQQHTVYIGIGSNIGDRMSHLREALAMLNNLESTSVTAISAIYMTEPVGEINQERFYNGV
LAVTTSMQPEALRQECKAIERTIGRPATYQRWSPRVIDLDLLLFDTLVCQTDTLAIPHPE
LHHRNFVLIPLLDIANPTHPLLGKSIRELLALCPDRSVLIKLQENIAL

For the Scan tools, enter a sequence motif using the single letter code for amino acids or nucleotides. See the article on search patterns for information about creating patterns for the scan tools.

For the BLAST tools, you may specify additional options in the Blast Options input box.

Search results include the name of the gene nearest the matched sequence. Neighborhood Width indicates how many base pairs in each direction from the center of the matched sequence will be searched to find a gene. This may be useful when searching for genes controlled by query operator sequences, for example.