 Overviews/Summaries |
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| Date of Assembly: 2009-05-23 | | Contigs: | | Number of Libraries: 3 | | Singletons: 5910 | | Number of ESTs: 358006 | | UniTrans: (Ctgs + Singles) | | Multi-Library Contigs: 14585 | | UniTrans = Unique Transcripts |
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| Source(s) of Annotation: plants_sp, plants_tr | | UniTrans w/ UniProt (UP): (90%) | | Date of Source(s): 2009-06-17, 2009-06-17 | | Contigs w/o UP: | | UniTrans w/ only MAIZE UP: | | Top Plant UP Count: | | UniTrans w/ UP but no MAIZE UP: | | Best UniProt Count: | | Best = UP is top match for a UniTrans w/ 1e-40 or better | | Potential Contamination: | | | | Top = UP is top-scoring match for a UniTrans |
 Library Descriptions | | | | Library | Cultivar | Tissue | # ESTs | # Contigs* | # Unique Contigs** | # Singletons |
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| ZM_BFa | B73 | mixed (silks, husks, ears, pollen, shoot tips, leaf, root tips, whole seed, embryo) | 19027 | | | | | ZM_BFb | B73 | mixed (silks, husks, ears, pollen, shoot tips, leaf, root tips, whole seed, embryo) | 227558 | | | | | ZM_BFc | B73 | mixed | 111421 | | | |
| | *Number of contigs that contain at least one EST from the library | | **Number of contigs that contain ONLY ESTs from the library |
| | Contigs w/ ESTs from all libraries: |
Additional Summaries/Example Queries | |
The above button goes to a page of tables displaying assembly statistics for Taxonomic Kingdom, Organism, UniProt, GO/GOSlim, protein pnemonic codes, contig characteristics and library comparisons via Test Statistic R by Stekel et al. Each of the tables offers quick links to the query producing the data so the user may modify the query to meet their particular needs. |
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Advanced Searches | | Common Queries: | | (e.g.) | Help | | | (e.g. ) | Help | | | (e.g. ) | Help | | | (e.g. ) | Help | UniTrans Query:
The PAVE-assembled contigs and singletons (i.e. UniTrans) can be filtered based any of the following criteria: Number of ESTs, Test Statistic R, presence of a complete ORF, number of mate pairs, GO annotation, SlimGO namespaces, UniProt match, length of contig and/or the expression levels of ESTs from specific libraries. Query examples given by links in the Library Descriptions table above. |
Protein Query:
This query gives the set of proteins most likely to be expressed by the libraries. To be included in the set, a UniProt ID must be the top match for a UniTrans, the UniTrans must match the UniProt ID with a E-value of 1e-40 or better and at least 60% of all UniTrans ESTs must match the UniProt ID. Only the best-formed contigs are included in this system. This query gives the most usable Test Statistic R values. |
No Anno Query:
When assemblies are annotated with a taxonomy-specific UniProt set the No Anno Query is made available for the contigs which did not receive a topmatch (E-value <= 1e-20) from the taxonomic UniProt blast. These unannotated contigs are blasted against the full UniProt database and the results are offered here. This query can be useful for identifying contamination contigs or potential discoveries. |
GO Query:
Query the GOs related to the strongly matched UniProt proteins. Query examples given by links in the GO by EST library table found on the Additional Summaries/Example Queries page (see link in previous section). |
| | Advanced Queries: | | (e.g. ) | Help |
Annotation Query:
This set of queries return results on all NRO matches, where the only restriction is that an organism can only be listed once for the set of hits for a given UniTrans (i.e. Non-Redundant Organism), and there are two separate NRO lists, one from Swiss-Prot and one from TrEMBL. Query examples are given by links in the Unique and Distinct NRO UniProt ID columns of the Annotation by EST library table found on the Additional Summaries/Example Queries page (see link in previous section). Use this query when searching for particular protein functions or for proteins seen in many species. |
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