NEMBASE is a resource for nematode transcriptome analysis, and a research tool for nematode biology, drug discovery and vaccine design.
NEMBASE4: The nematode transcriptome resource (open access article)
Benjamin Elsworth, James Wasmuth and Mark Blaxter. International Journal for Parasitology Volume 41, Issue 8, July 2011, Pages 881-894
Nembase4 was constructed in 2008 using 679,480 public nematode ESTs from NCBI. The core database was generated using the EST analysis pipeline PartiGene and has since been significantly modified. Contigs have been annotated using BLAST, annot8r and InterProScan.
| Table | Description |
|---|---|
| a8r_blastec | Enzyme annotations from annot8r |
| a8r_blastgo | GO annotations from annot8r |
| a8r_blastkegg | KEGG annotations from annot8r |
| blast | BLAST data |
| blast_top | Top BLAST hits |
| clone_name | Original EST name |
| cluster | Data for each EST cluster, including number of ESTs, contig number and consensus sequence |
| ec2description | Map of EC number and description |
| est | Data for each EST, including cluster ID, contig and library |
| est_seq | Seqeunce data for each EST |
| genome_pep | Data for each peptide including species, data origin and sequence |
| stage_count | Counts of ESTs per lifecycle stage for each cluster |
| hit_table | A combintation of cluster and BLAST information |
| interpro | InterProScan annotation results |
| interpro_key | Mapping information for InterPro and domain IDs |
| lib | EST Library information |
| lib_count | Counts of ESTs per library |
| lib_key | More library / spcies information |
| node2tribe | Tribe information for each node on the tribe_tree.php plot |
| node_stats | Overall tribe stats for each node |
| p4e_hsp | Prot4EST - information about high scoring pairs (HSPs) |
| p4e_ind | Prot4EST - main information table for each predicted peptide |
| p4e_loc | Prot4EST - details about the translation |
| pathway_id2name | KEGG ID to name map |
| pathway_map | Enzyme ID to EC number map |
| reciprocals | Reciprocal BLAST data |
| sex_count | Counts of EST per sex for each cluster |
| signalp | Signal peptide information |
| species | Species overview statistics |
| tribe | Tribe membership for each peptide |
| tribe_info | Stats for each tribe ID |
| tribe_node | Tribe node information |
| Table | Description |
|---|---|
| info | Detailed description of each species |
| org | The origins of the data for each species |
| species | Sequence, cluster and library counts for each species |
| stats | Statistics for each species |