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Malaysian Oil Palm Genome Programme (MyOPGP)
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Below are the available NCBI BLAST programs and their functions:
Compares a nucleotide query sequence against a nucleotide sequence database.
Compares an amino acid query sequence against a protein sequence database.
Compares a nucleotide sequence translated in all reading frames against a protein database.
Compares a protein query sequence against a nucleotide database translated in all reading frames.
Compares the six-frame translations of a nucleotide query against the six-frame translations of a nucleotide database.
The following reference databases are available for BLAST searches. Choose the one that best matches your query and analysis.
Contains 16 EG5 chromosomes (genetic scaffolds) and 40,056 P5 scaffold sequences. EG5 chromosomes were generated by comparing the P5-build to T128 and P2 genetic maps, with remaining P5 scaffolds also included.
Updated EG5 assembly in which 100-nt gap sequences (N) were introduced between scaffolds to build the 16 EG5.1 chromosomes.
Chromosome-scale EG11 assembly of E. guineensis, providing improved ordering and orientation of scaffolds compared with EG5.1 for downstream genome analyses.
Genome assembly for E. oleifera (EO12 build), supplied as chromosome-scale scaffolds for comparative BLAST analysis with E. guineensis.
Scaffold sequences from the E. oleifera O8-build.
Scaffold sequences from the pisifera P5-build.
Thirty transcriptome libraries were constructed and sequenced using Roche 454, 22 from E. guineensis and 8 from E. oleifera. Libraries for each species were assembled independently using Newbler.
Thirty transcriptome libraries were constructed and sequenced using Roche 454, 22 from E. guineensis and 8 from E. oleifera. Libraries for each species were assembled independently using Newbler.
Predicted nucleotide gene sequences (Version 3) from the pisifera P5-build with similarity to RefSeq proteins and support from oil palm transcriptome data.
Predicted amino acid sequences (Version 3) corresponding to the E. guineensis genes from the pisifera P5-build.
Genomic DNA from dura palms was used to create BACs. BAC clones were pooled into four pools (BAC9–BAC12) and sequenced using 454. Each pool was assembled separately and manually finished.
Contigs and singlets from assembled reads of E. guineensis genomic libraries.
Contigs and singlets from assembled reads of E. oleifera genomic libraries.
Amino acid sequences of predicted genes from the E. guineensis and E. oleifera GT contigs.
Nucleotide transcript sequences of predicted genes from the E. guineensis and E. oleifera GT contigs.
A sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. An example sequence in FASTA format is:
Sequences are expected to be represented in the standard IUB/IUPAC amino acid and nucleic acid codes, with these exceptions: lower-case letters are accepted and are mapped into upper-case; a single hyphen or dash can be used to represent a gap of indeterminate length; and in amino acid sequences, U and * are acceptable letters (see below). Before submitting a request, any numerical digits in the query sequence should either be removed or replaced by appropriate letter codes (e.g., N for unknown nucleic acid residue or X for unknown amino acid residue).
The nucleic acid codes supported are:
For those programs that use amino acid query sequences (BLASTP and TBLASTN), the accepted amino acid codes are:
The statistical significance threshold for reporting matches against database sequences; the default value is 10, such that 10 matches are expected to be found merely by chance, according to the stochastic model of Karlin and Altschul (1990). If the statistical significance ascribed to a match is greater than the EXPECT threshold, the match will not be reported. Lower EXPECT thresholds are more stringent, leading to fewer chance matches being reported. Fractional values are acceptable. (See parameter E in the BLAST Manual).