Net-tBlastN

Input
Remote DataBaseSelect 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.
Protein 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.
Perform gapped alignment Performs gapped alignment.
Setting this to OFF invokes the older, ungapped style of alignment.
You can't perform gapped alignments with tblastx, regardless of this setting.
Open Gap Cost   Initial penalty for opening a gap of length 0. -1 invokes the default behavior, and setting the parameter to zero is impossible, unless the "Perform gapped alignment" option is set to NO, which turns gapping off. The default gap costs for programs other than blastn depend on the scoring matrix.
Extend Gap Cost  The penalty for each gap character. Note that value -1 is synonymous with the default behavior for the "Open Gap Cost" parameter and, it's impossible to set value to zero unless the "Perform gapped alignment" option is set to NO, which turns gapping off. The default gap cost, for programs other than blastn, depends on the scoring matrix.
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.
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).
Composition-based statistics Use composition-based statistics for tblastn.
For programs other than tblastn, must be absent (Default).
Possible choices:.
1. Composition-based statistics as in NAR 29:2994-3005, 2001.
2. Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, conditioned on sequence properties.
3. Composition-based score adjustment as in Bioinformatics 21:902-911, 2005, unconditionally.