Finding cDNA clones: Difference between revisions
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Several partly overlapping initiatives have been generating and providing cDNA clones, i.e. reverse transcribed copies of mRNAs. Due to the academic or academic+commercial backbone of these enterprises, clones are available for relatively low costs, typically around 70€/50£/?$. As of 2008, clones are provided in Europe by '''GeneService''' and '''imaGenes''' (prev RZPD), and in N America by the '''ATCC/LGC''' Promochem. | Several partly overlapping initiatives have been generating and providing cDNA clones, i.e. reverse transcribed copies of mRNAs. Due to the academic or academic+commercial backbone of these enterprises, clones are available for relatively low costs, typically around 70€/50£/?$. As of 2008, clones are provided in Europe by '''GeneService''' and '''imaGenes''' (prev RZPD), and in N America by the '''ATCC/LGC''' Promochem. | ||
== Finding and checking candidate clones == | |||
There is a confusing number of cDNA clones and an even larger number of [[wikipedia:Expressed sequence tag|EST clones]] linked to most genes, esp. from humans and mouse. The tools below help you to select: | |||
== | * Many gene entries in the NCBI database are linked to cDNA clones. Look out for ''order cDNA clones'' (top right). Example: TUBB [http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&cmd=Retrieve&dopt=full_report&list_uids=203068] (human β-tubulin) and its NCBI-linked cDNA clones [http://www.ncbi.nlm.nih.gov/genome/clone/orderclone.cgi?db=gene&uid=203068]. | ||
* Check the [http://mgc.nci.nih.gov/ MGC (Mammalian Gene Collection)], a collection of full-length cDNA clones for human, mouse, rat, and cow genes. The MGC selects cDNA clones from various libraries if they satisfy their criteria for full-length clones. | |||
= | * Blast your mRNA of interest against a set of cDNA clones using for example the [http://www.imagenes-bio.de/blast RZPD/imaGenes tool]. The tool align known sequences from the clones with the mRNA search query which gives you an idea of whether you are looking at a full cDNA clone. | ||
* If you cannot find anything, have a look at the [http://www.ncbi.nlm.nih.gov/sites/entrez?db=unigene UniGene] entry for your gene. It contains an expandable list of EST clones (generally fragments for the full cDNA). Look out for the label '''PM''', which stands for could be translated into '''P'''rotein and is full length according to '''M'''GC. | |||
* query the [http://image.llnl.gov/image/html/query_tools.shtml IMAGE database], a now superseded consortium for the generation and distribution of cDNA clones; get the sequencing information for a clone of interest and align it to your mRNA of interested using tools like [http://www.ncbi.nlm.nih.gov/blast/bl2seq/ blast2seq] | |||
Revision as of 02:53, 12 February 2008
Several partly overlapping initiatives have been generating and providing cDNA clones, i.e. reverse transcribed copies of mRNAs. Due to the academic or academic+commercial backbone of these enterprises, clones are available for relatively low costs, typically around 70€/50£/?$. As of 2008, clones are provided in Europe by GeneService and imaGenes (prev RZPD), and in N America by the ATCC/LGC Promochem.
Finding and checking candidate clones
There is a confusing number of cDNA clones and an even larger number of EST clones linked to most genes, esp. from humans and mouse. The tools below help you to select:
- Many gene entries in the NCBI database are linked to cDNA clones. Look out for order cDNA clones (top right). Example: TUBB [1] (human β-tubulin) and its NCBI-linked cDNA clones [2].
- Check the MGC (Mammalian Gene Collection), a collection of full-length cDNA clones for human, mouse, rat, and cow genes. The MGC selects cDNA clones from various libraries if they satisfy their criteria for full-length clones.
- Blast your mRNA of interest against a set of cDNA clones using for example the RZPD/imaGenes tool. The tool align known sequences from the clones with the mRNA search query which gives you an idea of whether you are looking at a full cDNA clone.
- If you cannot find anything, have a look at the UniGene entry for your gene. It contains an expandable list of EST clones (generally fragments for the full cDNA). Look out for the label PM, which stands for could be translated into Protein and is full length according to MGC.
- query the IMAGE database, a now superseded consortium for the generation and distribution of cDNA clones; get the sequencing information for a clone of interest and align it to your mRNA of interested using tools like blast2seq
