Table 2 Access to the Salmon Genome Project web resources.
Salmon Genome Project (SGP) data resource | |
|---|---|
Option name and description | Access from menu on the main page |
SGP data and results statistics | Data and results > Results > General statistics; Sequence length statistics Data and results > cDNA libraries > SGP libraries list short; SGP libraries list full |
Database search SGP database text queries on sequence descriptions and annotations best hits, or searches of the SGP and NCBI sequence databases (Sequence search) | Database search > Simple search; Advanced search; Sequence search |
ESTs submitted to GenBank | Data and results > Results > EST sequences in GenBank; Sequences in UniGene |
cDNA libraries Description and number of ESTs in SGP libraries, pre-processed sequences, clustered and singlet sequences, sequences submitted to GenBank | Data and results > cDNA libraries > SGP libraries list short; SGP libraries list full > select library Data and results > cDNA libraries > SGP libraries > select library |
Clustered data datasets Description and access to database snapshots of clustering and automatic annotation results for specific sets of data | Data and results > Clustered data datasets |
Clustered data summary Clustering data and annotation best hits results for datasets Contigs and singlets annotation Contigs length and number of reads | Data and results > Clustered data summary > SGP > > Contigs and best annotation hits; Singlets and best annotation hits > Contigs length and number of reads; Distribution of average length and number of reads in contigs |
Contig and singlet sequences Singlets and contig consensus sequences resulting from contig assembly of data from SGP cDNA libraries | Data and results > Clustered data datasets > Contigs; Singlets Data and results > cDNA libraries > SGP libraries (or select library) > Clustered and singlets sequences SGP Database > Search SGP database > Advanced search |
Annotations Detailed BLAST-GO automatic annotation results and annotation statistics for datasets | Data and results > Annotations Database search > Simple search; Advanced search |
preAssemble Pre-assembly automatic sequencer data processing pipeline available as a web-based tool and for downloading | SGP workbench > preAssemble Supplemental > Download preAssemble |
SGP local BLAST server BLAST queries against the SGP local database, Salmonidae-specific and other NCBI datasets | SGP workbench > Blast search |