UC-Target selection: Select suitable targets
| Summary: | The process of selecting targets for protein production and
crystalization, requires that the scientist screens potential target
sequences against various criteria which may influence expression. The criteria will vary, depending on the overall aims of the research project, but may include: - the presence/absence of certain sequence motifs such as recognition sites for glycosylation and cleavage by proteases - the presence of homologous structures already determined Remote sites for this purpose include the OPPF's OPAL -Oxford Protein Analyser Linker Tool (to be implemented in PIMS), and the YSBL's Target Selection Resource |
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| Importance: | Desired |
| Priority: | Desired |
| Use Frequency: | Sometimes |
| Direct Actors: | Experimenter |
| Main Success Scenario: |
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| Variations |
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| Notes and Questions |
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UC-BLAST sequence: Perform BLAST search for a sequence
| Summary: | An experimenter will often wish to perform BLAST (Basic Local Alignment
Search Tool: Altschul et.al.1990) searches of a protein (or DNA) sequence for
similarity in a (usually) remote sequence database. This is typically performed during the target selection process, for example to determine if homologues to a proposed target exist. BLAST searches are also performed periodically, following target selection, to search for recently sequenced homologues and solved structures. See the NCBI BLAST service web page for possible programs or the EBI's Similarity Searching and Homology TOOLS selection page See also Jamie Prilusky's SeqAlert service which compares a sequence(s) against PDB and TargetDB. |
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| Importance: | Expected |
| Priority: | Desired |
| Use Frequency: | Often |
| Direct Actors: | Experimenter |
| Main Success Scenario: |
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Alternative 1a Scenario Extensions: |
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| Variations |
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| Notes and Questions |
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UC-Design primers: Design PCR primers
| Summary: | An experimenter will frequently need to design primers for PCR and
sequencing experiments. A number of remote websites and commercial software
aplications exist for this purpose. Different laboratories will have preferences. For example Invitrogen Vector-NTI softwareis used by some MPSI labs. The Whitehead Institute's Primer3 is a widely used web based service which could be integrated. |
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| Importance: | Expected |
| Priority: | Desired |
| Use Frequency: | Often |
| Direct Actors: | Experimenter |
| Main Success Scenario: |
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Alternative 1a Scenario Extensions: |
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| Notes and Questions |
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UC-Order primers: Order primers from supplier
| Summary: | After designing PCR primers, an experimenter may wish to have them
synthesized. This may be an "in house" or a commercial service.
On-line primer ordering services are available e.g. MWG Biotech provides downloadable order form templates. The details can then be entered into PIMS |
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| Importance: | Desired |
| Priority: | Desired |
| Use Frequency: | Sometimes |
| Direct Actors: | Experimenter |
| Main Success Scenario: |
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Alternative 1a Scenario Extensions: |
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| Notes and Questions |
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UC-Genomic DNA available: Check genomic DNA availability
| Summary: | When selecting targets, experimenters may need to check the availability
of genomic DNA from the species of interest. ATCC_LGC provides a searchable distribution service. |
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| Importance: | Desired |
| Priority: | Expected |
| Use Frequency: | Rarely |
| Direct Actors: | Experimenter |
| Main Success Scenario: |
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| Notes and Questions |
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UC-cDNA available: Check cDNA availability
| Summary: | When selecting eukaryotic targets, experimenters may need to check the
availability of cDNAs encoding full-length proteins of interest. For mammalian proteins (human, rat and mouse) the Mammalian Gene Collection MGC provides a searchable list of full-length clones. These are available through the IMAGE (Integrated Molecular Analysis of Genomes and their Expression) Consortium clone distribution network, along with a list of authorized distibutors in Europe and the USA. Human and mouse clones also available from the Invitrogen Ultimate ORF collection. Arabidopsis cDNAs can be obtained from the European Arabidopsis Centre NASC Also see LocusLink for curated sequence and descriptive information about genetic loci from a number additional eukaryotes |
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| Importance: | Desired |
| Priority: | Expected |
| Use Frequency: | Rarely |
| Direct Actors: | Experimenter |
| Main Success Scenario: |
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| Notes and Questions |
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UC-Is target registered: Check if target is registered in Targetdb
| Summary: | To avoid duplication of effort, an experimenter will need to determine if
a potential target has been registered in the
TargetDB database. This provides a registration and tracking information for a large number of structural genomics and proteomics projects worldwide including SPINE and OPPF. This may be included in UC-Target selection: Select suitable targets |
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| Importance: | Desired |
| Priority: | Desired |
| Use Frequency: | Sometimes |
| Direct Actors: | Experimenter |
| Main Success Scenario: |
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| Notes and Questions |
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UC-Align sequences: Perform sequence alignment
| Summary: | An experimente may wish to align a number of protein (or nucleotide)
sequences. This can be to find regions of similar sequence which define a
conserved domain or pattern, or to derive possible evolutionary relationships
among the sequences. This may be included in UC-Target selection: Select suitable targets, and is often performed on the results from a BLAST search. UC-BLAST sequence: Can be performed using locally installed software, or at remote servers e.g. the EBI's ClustalW sequence analysis tool, which has an option to retrieve the results by e.mail |
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| Importance: | Desired |
| Priority: | Desired |
| Use Frequency: | Sometimes |
| Direct Actors: | Experimenter |
| Main Success Scenario: |
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Alternative 1a Scenario Extensions: |
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Alternative 2a Scenario Extensions: |
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| Notes and Questions |
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UC-Predict TM helices: Predict TM helices in a protein
| Summary: | When selecting targets, experimenters may need to determine the number
and location of transmembrane (TM) helices A service is provided at a number of remote sites which use HMMs (Hidden Markov Model) algorithms. For example, run TMHMM at the CBS site in Denmark. TM prediction can also be performed on multiple sequences. For example HMMTOP is performed following a ClustalW alignment. TM predictions may be part of the target selection process UC-Target selection: Select suitable targets |
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| Importance: | Desired |
| Priority: | Desired |
| Use Frequency: | Sometimes |
| Prereq: |
User must belong to a user group with appropriate access rights
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Main Success Scenario: |
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Alternative 5a Scenario Extensions: |
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| Notes and Questions |
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UC-name: USE CASE NAME
| Summary: | 1-3 SENTENCES |
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| Importance: | Essential | Expected | Desired | Optional |
| Priority: | Essential | Expected | Desired | Optional |
| Use Frequency: | Always | Often | Sometimes | Rarely | Once |
| Direct Actors: | ACTOR1, ACTOR2, ACTOR3 |
| Prereq: |
PRECONDITION
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| Main Success Scenario: |
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Alternative "index" Scenario Extensions: |
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| Variations |
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Retain this copyright statement whenever this file is used as a
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