The I.M.A.G.E. Consortium
"Sharing resources to achieve a common goal - the discovery of all genes"
The I.M.A.G.E. Frequently Asked Questions Page
How can I get an I.M.A.G.E. Consortium clone sent to me?
Simply contact one of
our authorized distributors and order
the clone(s) from them, using the I.M.A.G.E. CloneID to
specify which clone(s) you are interested in. You can check for clone availability at http://image.llnl.gov/image/bin/availablePlatesNew.
Does I.M.A.G.E. have an FTP site?
Yes. Just ftp to image.llnl.gov and change to the image directory to get to the I.M.A.G.E. ftp site. Or, if your
browser supports it, just click on the following link: ftp://image.llnl.gov/image
This is an anonymous ftp server so use "anonymous" to login and your email address as password.
Some files of interest include:
Plate data: includes information for every cloneID on plate location, library, species and Genbank accessions. Data is updated nightly, with monthly cumulative files. The same information is also available for rearrayed clones .
Library data: lists data for each library, including library name, organism, tissue source, cloning details and host strain. Data is updated nightly, with monthly cumulative files.
Vector data: includes data on vector name, antibiotic resistance and source. Data is updated nightly, with monthly cumulative files.
Sequence-verified clones : list of clones which have been verified by sequence end-reads. New files are generated weekly.
Problem clones: list of clones which have had problems reported by any source (not verified by I.M.A.G.E.). New files are generated weekly.
If you have additional data requests, please send an email to help@image.llnl.gov.
What tools are available to query the I.M.A.G.E. dataset?
In response to requests for help querying the large I.M.A.G.E. dataset, informatics staff have developed as set of web-based tools.
These include the IQ, a general-purpose clone and library query tool and IMAGEne, a sequence clustering and alignment program.
Additional tools have been developed by our collaborators. The Mammalian Gene Collection websites (MGC for human, mouse, rat and cow; XGC for Xenopus and ZGC for zebrafish) allow you to search for full-length MGC clones by gene symbol or keyword, do a nucleotide BLAST against full-length clones, download the full-length clone and sequence list, and view all ESTs and candidate full-length genes.
Why aren't all the I.M.A.G.E. clones immediately available from the distributors any more? How can I find out which ones are?
Due to the high levels of redundancy in the human and mouse MGC collections,
clones from those species arrayed for 5' sequencing since October 2002 (production plates LLAM, LLCM, and LLKM) are no longer routinely available from the IMAGE Consortium distributors. Please note the following changes, effective October 2002:
- All human and mouse MGC clones have an 8-digit IMAGE identifier to
distinguish them from clones arrayed prior to this date, which have 5, 6, or 7
digit identifiers.
- Only human and mouse clones sent out for full-insert sequencing are
available from all IMAGE distributors on a routine basis (as before). To see if a particular clone is included in the completely sequenced set, please check ftp://image.llnl.gov/image/outgoing/ND_available_clones.txt.
- Human and mouse MGC clones not sent out for full-insert sequencing
and which are non-redundant (one whose sequence is unique, i.e. no other clone
from the same species contains an identical sequence) can still be ordered directly from the IMAGE distributors, but will require additional processing time. Please contact their help desk directly as the clones may not be listed online.
Some distributors have elected to discontinue receiving EST clones from zebrafish and Xenopus; however, the clones are still available as special-order items through those distributors (but may not be available on their website). In addition, cow ESTs are only available through Open Biosystems, or as special-order items through any of the other four distributors. ALL DISTRIBUTORS RECEIVE ALL FULL-LENGTH CLONES, REGARDLESS OF SPECIES.
You can check for clone availability at http://image.llnl.gov/image/bin/availablePlatesNew.
If you are unable to obtain a clone, please send an email to help@image.llnl.gov.
Which number in a database entry is the I.M.A.G.E. CloneID?
This depends a bit on which database you are retrieving sequence
data from...
In dbEST entries, the I.M.A.G.E. CloneID is the number given in
the "CloneID" field. In most cases the ID is prefaced by the word IMAGE.
In GenBank entries, the I.M.A.G.E. CloneID is the number
in the Definition line. In most cases the ID is prefaced by the word IMAGE. It can also be found in the Features section on the \clone line.
Why are there so many accession numbers and IDs associated with each clone? What do they all mean?
The I.M.A.G.E. cloneID is a unique identifier assigned by I.M.A.G.E. to each clone. All sequences derived from a given clone will reference the same I.M.A.G.E. cloneID, and there may be more than one Genbank entry for a given I.M.A.G.E. cloneID (ie one for the 5' EST, one for the 3' EST, one for the full-insert sequence, etc). Each sequence entry gets a unique Genbank accession number and a unique GI number (both assigned by the NCBI). All full-length MGC sequence entries are also assigned a unique MGC ID by the Mammalian Gene Collection project. A subset of mouse clones have been assigned an MGI ID from the Jackson Laboratory. The I.M.A.G.E. distributors may also assign internal tracking IDs to the clones. When in doubt, you can ALWAYS use the I.M.A.G.E. cloneID to order the clone you want and as this is the simplest and most straightforward option, this is what we encourage everyone to do.
I know a certain IMAGE clone is in the NCBI database, but its sequence doesn't appear in the IMAGE database. Why?
Any information we have that comes from NCBI is gathered through a nightly process that we have built to collect data from their databases. It is achieved by parsing all the records in the EST, Primate (PRI), Rodent (ROD), Vertebrate (VRT) and Synthetic (SYN - for ORF clones) sections of Genbank and looking for those that relate to our clones. It goes without saying that the English language does not lend well to a predictable set of rules and therefore we must make certain assumptions in order to parse, store and then deliver data to you. If a submitter isn't aware of the assumptions we must make in order to parse the record then it won't get into our database. We have available a document for submitters that can serve as a guildline for them. It is of course impossible for us to get all data collected on IMAGE clones under the current format of Genbank records, but we do manage to get a very high percentage because our format requirements are generally adhered to by the mass volume sequencing centers that we are in contact with.
Sequences from IMAGE clones with certain types of errors (chimeric, frameshifted etc) are submitted to the HTC division of Genbank and those are not included in our database. You can access them by an Entrez search using the IMAGE cloneID in the format (including double-quotes) "IMAGE:XXXXXXX".
Now that I have a clone, where can I find information about
the vector, cDNA library, antibiotics, etc.?
The I.M.A.G.E. homepage, under the "resources" link, contains
a vector list which
includes - to the extent we know them - vector sequences,
polylinker sites, appropriate sequencing primers, and the like.
There are also links to library pages,
which are organized by species, or you can use the Library Navigator to select libraries by
tissue or library name. Your clone distributor may also be contacted.
Am I restricted in what I can do with an I.M.A.G.E. clone?
Only by your imagination - almost ... the key is that we
are providing clones to advance the public interest. A
Good Faith Agreement governs the usage of
I.M.A.G.E. clones. Basically you may use an I.M.A.G.E. clone for any
purpose, but you may not sell the clone itself (you may pass it on for
free to anyone else as long as the person receiving it agrees with these
same stipulations. In general, we discourage secondhand distribution since clone quality suffers (deleted clones, contaminated stocks, etc.) unless
quite a bit of care is taken.) We also encourage people to submit sequence, map, and expression data derived from the use of this clone to an appropriate
public database, and you associate this information with the pre-existing unique identifier (I.M.A.G.E. CloneID). We also encourage you to sequence (at least the ends of) any clone you receive, and to immediately inform the distributor of any discrepancies.
Are there restrictions on inventions (ie patents) using these clones?
No, the I.M.A.G.E. Consortium does not place any restrictions on inventions. Any invention based on the use of these clones belongs
solely to the inventing party. You may take any reasonable
steps necessary to protect your proprietary interests before
submitting information to public databases.
How can I get aliquots of the library from which a given
I.M.A.G.E. clone is derived?
This depends on the source of the original (unarrayed) library. Libraries from commercial sources are usually available for sale through that company. Libraries donated by academic groups may be available from that group, or under certain circumstances may be available directly from LLNL. To find the source of a particular library, check the description for that library on the library webpage (organized by species), or send an e-mail to
help@image.llnl.gov
indicating which library you are interested in and we
will forward the name of the appropriate contact person.
Please be aware that some libraries are not available, and unless
the distributor is also the library source, library aliquots are not
available through the five distributors.
Is there a bibliographic reference for the I.M.A.G.E. effort?
Yes: Lennon, G.G., Auffray, C., Polymeropoulos, M., Soares, M.B.
The I.M.A.G.E. Consortium: An Integrated Molecular Analysis of
Genomes and their Expression. Genomics 33:151-152 [1996].
How can I check for reported problems on a clone?
Problem clone data
can be found on the I.M.A.G.E. webite. The available data integrates
all problems reported to or by the I.M.A.G.E. Consortium and have not been
independently verified. As always, any problems you encounter with a clone
should first be reported to the distributor from which it was obtained, and if the problem is not resolved to your satisfaction, you are encouraged to report the problem to help@image.llnl.gov.
What if I have further questions?
Our goal of being able to help integrate genome studies - using
publicly available data, from royalty-free cDNA clones - is being
reached thanks to your support and enthusiasm, and we always
welcome questions, comments, and suggestions to:
help@image.llnl.gov
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