For more information, visit the bEST web site.
Remaining ESTs not covered by the GO associations relied on matches to the NCBI non-redundant database (release 144) to approximate candidate gene assignments. BlastX better for matches, but BlastN better for gaining additional candidate assignments.
The matches to the NR release 144 database were then matched to descriptions to the NCBI Clusters of Orthologous Groups (COG) Index (www.ncbi.nlm.nih.gov/COG/) to finish out the descriptions. Of the 4,992 searched against the NR database, most unusually matched to the database and were attempted to be placed in functional categories as classified for the NCBI COG Index; 560 apparently did not have matches, but even so, most of these did match sequences in plant EST databases.
5548 sequences not GO assigned were extracted and assigned by NR keyword matches to the COG tables and micellaneous categories. There were 550 not assigned by this method, but did have matches to the NR database, and upon inspection would fit into the general genome sequence class; there were only 10 sequences of the entire collection which did not have any matches to either the UniProt or the NR database.
| INFORMATION STORAGE AND PROCESSING | ||
| 85 | J | Translation, ribosomal structure and biogenesis |
| 2 | A | RNA processing and modification |
| 47 | K | Transcription |
| 2 | L | Replication, recombination and repair |
| 5 | B | Chromatin structure and dynamics |
| (2.5%) | ||
| CELLULAR PROCESSES AND SIGNALING | ||
| 4 | D | Cell cycle control, cell division, chromosome partitioning |
| . | Y | Nuclear structure |
| 3 | V | Defense mechanisms |
| 8 | T | Signal transduction mechanisms |
| 3 | M | Cell wall/membrane/envelope biogenesis |
| 1 | N | Cell motility |
| 17 | Z | Cytoskeleton |
| . | W | Extracellular structures |
| 3 | U | Intracellular trafficking, secretion, and vesicular transport |
| 22 | O | Posttranslational modification, protein turnover, chaperones |
| (1.1%) | ||
| METABOLISM | ||
| 12 | C | Energy production and conversion |
| 13 | G | Carbohydrate transport and metabolism |
| 78 | E | Amino acid transport and metabolism |
| 3 | F | Nucleotide transport and metabolism |
| . | H | Coenzyme transport and metabolism |
| 8 | I | Lipid transport and metabolism |
| 9 | P | Inorganic ion transport and metabolism |
| 8 | Q | Secondary metabolites biosynthesis, transport and catabolism |
| METABOLISM | ||
| 94 | R | General function prediction only |
| 2 | S | Function unknown |
| (2.4%) | ||
| MISCELLANEOUS CATEGORIES OF INTEREST | ||
| 2 | XS | Storage |
| 7 | XT | Repetitive |
| 10 | Sorghum Genome | |
| 349 | Zea mays Genome | |
| 3107 | Oryza sativa Genome | |
| 111 | Triticum spp. Genome | |
| 1 | Pennesetum spp. Genome | |
| 94 | Hordeum spp. Genome | |
| 67 | Saccharum spp. Genome | |
| 154 | Arabidopsis thaliana Genome | |
| 397 | Mus musculus Genome | |
| 179 | Homo sapiens Genome | |
| 81 | XG | General Genome |
| (82.2%) | ||
| 560 | X | Other |
| (10.1%) | ||
| 5548 | Total | |