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Searching Lumbribase
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Searching by Sequence Id
You may retreive specific clusters by entering the sequence identifier in the text box. Any LumbriBASE, EandreiBASE or wormbase identifier
may be used to search. |
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Searching specific libraries
This page allows you to search specific EST libraries in Lumbribase by expression level and view the results as either a table of
expression levels, balst results, or as a SimiTri profile for a large number of clusters on a single graphic.
- Choose the required expression level for each library.
- 0 means clusters not expresed in that library
- blank means no selection criteria is imposed
- otherwise >5, <5 or 5 are valid formats.
- Select the type of output required and for the SimiTri output select the Type of data you wish to display.
- Bit score comparison between sequence databases of other species.
- expression level differences between libraries
- Submit the search.
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Searching by Sequence Similarity
This page allows you to retrieve clusters with sequence similarity to a specified sequence using BLAST.
- Choose the appropriate 'Program' and options.
- Enter your sequence in FASTA format and select your appropriate output view options.
- Click on 'Search' to perform your BLAST.
After a few moments you will see the blast output. The cluster number links to all the available information for that cluster.
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Searching for large clusters
This search allows you search for clusters which contain a minimun number of ESTs. Just select a database and enter a number over 10 in the input box.
We don't allow this search to include clusters with less than 10 ESTs because there are so many of them it slows our server too much. |
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Searching protein sequence digests with a Peptide Mass Fingerprint
This is only available for Lumbribase and Wormpep proteins
- Enter a list of peptide masses, delimited with either comma, space or new line.
- Select the protein database to search, L. rubellus, C. elegans or both.
- Mass Values
- monoisotopic; The lowest common isotope for each element is used for the mass calculation
The masses asigned to each protein are from a theoretical trypsin digest with AND without modifications...
- Peptide N-terminal Gln (Q) to pyroGlu (E)
- Oxidation of methionine
- Protein N-terminus Acetylated
- Carbamidomethylation
- average; All the isotopes for each element are used, with their abundances reflecting their "normal" proportion in the biosphere.
- Digest; The protease used to digest the proteins in the database. Currently only a trypsin digest is available.
- Peptide tolerance; To set the stringency of your search, lower figures are more stringent. This tolerance can be
represented as %, ppm, Da etc. We use ppm (parts per million) and normally set it at 50. The value should reflect the accuracy of the
mass spec that you use and how well you calibrate your samples. This means that searching for a peptide fragment of 1000.00 Da with the
tolerance set at 100ppm you will search between 999.90 Da and 1000.10 Da. Apparently mass specs have a mass dependant error associated
with the mass measurement so using relative values like ppm is better than using absolute values such as Daltons.
- Results; The number of results to report. Results are sorted by the number of fragment matches, restricting
the number reported only shows the best matches.
- Minimum fragments match; Minimum number of fragments that must match for a protein to be reported.
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Plate reference search
For a limited number of C. elegans sequences you can enter either the 96 or 384 plate well reference or the wormbase sequence identifier to
get the other references returned. |
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Primer seuqence search
For a limited number of C. elegans sequences you can enter either the 96 or 384 plate well reference or the wormbase sequence identifier to
get the forward and reverse primer sequences returned. |
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