Do you have suggestions for using Gene Search and BLAST tools to find cDNA clones?
1.) Performing a standard gene query using our gene search tool.
a.) Use gene symbol(s), accession numbers, or clone IDs. Unfortunately, duplicates do exist so refer to the Oligo/Clone ID when identifying whether or not a clone is truly a duplicate. IMAGE ID is a unique identifier given to each cDNA clone by the I.M.A.G.E. Consortium.
b.) cDNA clones are referenced against a GenBank accession number. Full length cDNA clone accessions typically begin with the ‘BC’ prefix. These clones have been derived from tissue, are fully sequenced (we guarantee the sequence will match NCBI’s record), and are different from RefSeq accession numbers (beginning with ‘NM_’ prefix). From NCBI’s website:
“The Reference Sequence (RefSeq) database is a non-redundant collection of richly annotated DNA, RNA, and protein sequences from diverse taxa. The goal is to provide a comprehensive, standard dataset that represents sequence information for a species. It should be noted, though, that RefSeq has been built using data from public archival databases only. RefSeq biological sequences (also known as RefSeqs) are derived from GenBank records but differ in that each RefSeq is a synthesis of information, not an archived unit of primary research data. Similar to a review article in the literature, a RefSeq represents the consolidation of information by a particular group at a particular time.”
c.) Clone IDs are IMAGE IDs, not MGC IDs.
d.) Restriction enzymes, vector map, sequence, and other useful information is available by clicking on the blue "+" for each result opens tabs below including "details".
e.) Clicking on the Accession number for each result opens the NCBI record on a new tab
f.) Clicking on the vector in the "details" tab for each result opens the vector map”.
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2.) Use our BLAST tool to find clones by amino acid or nucleotide sequence - also will find 'non-queryable' clones (We have cDNA collections whose data was not submitted to GenBank, thus the clones do not have GenBank accession numbers.)
a.) Choose BLAST tType "Nucleotide" to work with nucleotide sequences.
b.) When working with a protein sequence, choose "Peptide" for your BLAST Type.
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3.) Using NCBI for BLAST and to find protein/gene information
a.) http://www.ncbi.nlm.nih.gov/BLAST/ is the link for NCBI’s multiple BLAST options. As mentioned, you can search nucleotides using protein accession numbers and vice versa. At the bottom of the page is an option to perform a pairwise BLAST, which is aligning two sequences. http://www.ncbi.nlm.nih.gov/BLAST/bl2seq/wblast2.cgi
b.) Searching on NCBI using gene name, gene symbol, accession number (either RefSeq or GenBank), or protein accession (NP_ for protein against NM_ or other prefix against GenBank accession number) offers numerous options for searching to find information. One of the most comprehensive views is via Entrez, which will provide all related sequences and proteins to that particular gene.