NetBlastN

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.
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.
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
MegaBlast search Sets the blastn program to the megablast mode, which is optimized to find near identities very quickly.
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.
Nucleotide Mismatch Penalty   Sets the penalty for a nucleotide mismatch. Also see "Nucleotide Match Reward". The choice of [integer] for "Nucleotide Mismatch Penalty" and "Nucleotide Match Reward" are very important because they determine your target frequencies. The default values 1 for "Nucleotide Match Reward" and -3 for "Nucleotide Mismatch Penalty" are most effective for aligning sequences that are 99 percent identical.
Nucleotide Match Reward   Sets the score of a nucleotide match. See also the "Nucleotide Mismatch Penalty" parameter.
Number of DB Seqs to show descriptions   Sets the number of database sequences for which to show the one-line summary descriptions at the top of a BLAST report. You won't be warned if you exceed a value. Also see the "Number of Alignments to output" parameter.
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).