CGD Multi-Genome Search
using NCBI BLAST+

using Default Settings:

• All genomes searched
• Gene sequences searched with BLASTN for DNA query
• Protein sequences searched with BLASTP for protein query

Select or unselect multiple genomes by pressing the Control (PC) or Command (Mac) key while clicking.

NOTE: Dataset options may be limited by Target Genomes choice. Datasets for non-coding sequence features are currently only available for the following genomes:

To search specifically for non-coding features, limit your choice to these genomes. To search for non-coding features in other genomes, choose the "GENOME" dataset.

NOTE: Program options are limited by Query Sequence type and Target Sequence Dataset choice. We try to guess your Query Sequence type from its text content. If that guess is wrong, you can override it here:

NOTE: Since not all of the genomes are fully annotated yet, with protein queries you may get more comprehensive results searching the "GENOME" datasets using the TBLASTN program.

NOTE For BLASTX and TBLASTX searches:
You may choose an alternate genetic code to use for query translation. Queries for which this may be appropriate include DNA sequences from most Candida-related species (use 12: Alternative Yeast Nuclear Code) or mitochondrial DNA sequences. See the Non-standard Genetic Codes Help Page for more details. The default code for CGD is: 12: Alternative Yeast Nuclear Code.

Optional BLAST Parameters
For descriptions of BLAST parameters and search strategies, refer to the BLAST documentation at NCBI.
For specification of the default parameter values used by CGD, please see the BLAST default parameter help page.


Number of alignments to display:
0 10 25 50 100 250 500


Set Expect Threshold (E-value):
1e-20 1e-10 0.0001 0.01 1 10 100 1000


Choose a search strategy:
Default for program and query length MEGABLAST - Highly similar hits DC-MEGABLAST - Similar hits BLASTN - Distant hits BLASTN-SHORT - Query less than 50 nt
NOTE: BLASTN and BLASTP searches only.
For BLASTN, the default strategy is DC-MEGABLAST except for queries < 50 nt (BLASTN-SHORT).
For BLASTP, the default strategy is BLASTP except for queries < 30 aa (BLASTP-SHORT).
Choice may alter the default values for the parameter settings below.


Low-complexity filtering:
default On Off DUST for BLASTN, SEG for all others
Allow gapped alignments?
default Yes No
Choose nucleotide match/mismatch scores:
default 1/-4 1/-3 1/-2 2/-3 4/-5 1/-1 Applies to BLASTN only
Choose amino acid substitution matrix:
default PAM30 BLOSUM45 BLOSUM50 BLOSUM62 PAM70 BLOSUM80 BLOSUM90 PAM250 Applies to all programs except BLASTN
Set BLAST word length:
default 7 9 11 13 16 20 24 28 32 48 64 128 256