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Net-tBlastX |
| Input | |
| Remote DataBase | Select remote DB:
Non-Redundant - All GenBank, EMBL and DDBJ Non-Redundant sequences (but no EST, STS, GSS, or phase 0, 1 or 2 HTGS sequences). WGS entries are also excluded. No longer "Non-Redundant". EST - Database for entries from Estimated Sequence Tags (EST) division of GenBank, EMBL and DDBJ. Human EST - H.Sapiens subset of Estimated Sequence Tags. Mouse EST - M.Musculus subset of Estimated Sequence Tags. Other EST - EST other than Human or Mouse. GSS - Genomic Survey Sequence, includes single-pass genomic data, exon-trapped sequences, and Alu PCR sequences. HTGS - Unfinished High Throughput Genomic Sequences: phases 0, 1 and 2. Finished, phase 3 HTG sequences are in NR. Patented sequences (PAT) - Nucleotides from the Patent division of GenBank. Monthly Sequences (Month) - All new or revised GenBank, EMBL and DDBJ sequences released updated in the last 30 days. Alu repeats - Select Alu repeats from REPBASE, suitable for masking Alu repeats from query sequences. STS - Database of GenBank, EMBL and DDBJ sequences from STS Division. Chromosomic Sequences - Complete genomes, complete chromosomes, or concatenated genomic contigs from NCBI Reference Sequence Project. Vector fragments (UniVec) - The UniVec non-redundant vector fragment sequences. Whole Genome Shotguns (WGS) - Whole Genome Shotgun sequence assembly. Custom - Specify the database of your interest. |
| Nucleotide Query sequence(s) | If the input file contains multiple sequences, BLAST will be run on each sequence in order, and the resulting output will contain concatenated BLAST reports. |
| Believe the query defline. | Believe the query definition line. |
| Output | |
| Result | Designates an output file for the search results. |
| Format |
Pairwise (Default)
Query-anchored, showing identities Query-anchored, no identities Flat query-anchored, showing identities Flat query-anchored, no identities Query-anchored, no identities and blunt ends Flat query-anchored, no identities and blunt ends XML Blast output Tabular Tabular with comment lines ASN, text ASN, binary |
| Show GI's in deflines | Shows GenInfo Identifier (GI) numbers in definition lines.
A GI is a unique numeric identifier assigned for a sequence in GenBank. A GI corresponds to an accession version pair. |
| Produce HTML output |
Produces HTML output with [anchor] links from
the summary at the top of the report to the
alignments farther below.
This option should be used only with the standard report format ("Pairwise (Default)"). |
| Options | |
| Expectation value |
Sets the threshold expectation value for keeping alignments.
This is the E from the Karlin-Altschul equation that describes how often an alignment with a given score is expected to occur at random. |
| Filter query sequence |
Filters the query sequence for low-complexity subsequences.
The default setting is ON. Complexity filtering is generally a good idea, but it may break long HSPs into several smaller HSPs due to low-complexity segments. This can cause some alignments to fall below the significance threshold and be lost. To prevent this, either turn off filtering (not recommended) or use soft masking, in which the filter is used only in the word seeding phase, but not the extension phase. DUST with blastn, SEG with others. |
| Translation table | Select translation table. |
| DB Genetic code |
The genetic code to use for translation of the database nucleotide sequence.
See http://www.ncbi.nlm.nih.gov/htbin-post/Taxonomy for updates |
| Matrix |
Designates a protein similarity matrix.
This is used in all BLAST programs except blastn. Matrices are sought in the following order: in the local directory, in the location specified in the .ncbirc file, in a local data directory, and finally, in the BLASTMAT environment variable (only on Unix systems). Other matrices included in the standard distribution include BLOSUM45, BLOSUM80, PAM30, and PAM70. You can use custom matrix files, but it requires modifying the source code and defining the new matrix with all of its associated statistics for different affine gap combinations and recompiling the binary. Using these custom files isn't recommended because it requires the arduous task of calculating gapped values for lambda and maintaining a derivative branch of the source code. |
| Query strands | Chooses which strand of DNA-based queries
is searched.
Top Strand Bottom Strand Both Strands |
| Location on query sequence |
The location on query sequence. This lets you limit the search to a subsequence of the query sequence. For example, to search just the letters from 21 to 50, set the parameter to following: "21,50". The alignments won't extend outside the specified region. In older versions of BLAST, this parameter set the size of the region under control of the "Best Hits Number" parameter. |
| Search Space Effective Length | Effective length of the search space. Use zero for the real size (Default). |