Needleman-Wunsch alignment of two nucleotide sequences [?]

Alignments may be classified as either global or local.A global alignment aligns two sequences from beginning to end, aligning each letter in each sequence only once.An alignment is produced, regardless of whether or not there is similarity between the sequences.
A local alignment can also be used to align two sequences, but will only align those portions of the sequences that share similarity. If there is no similarity, no alignment will be returned. Local alignments algorithms (such as BLAST) are most often used. A global alignment should only be used on sequences that share significant similarity over most of their extents, and then it will sometimes return a better presentation.
An example is the alignment of NP_004013 with NP_004014. These are both dystrophin isoforms, but the first sequence is missing about 100 residues starting at residue 948 (some exons have been spliced out of the corresponding mRNA). A global algorithm returns one alignment clearly showing the difference, a local algorithm returns two alignments, and it is difficult to see the change between the sequences. The global alignment at this page uses the Needleman-Wunsch algorithm. The algorithm also has optimizations to reduce memory usage.

Enter Query Sequence
Enter query sequence(s) in the text area. It automatically determines the format of the input. To allow this feature, certain conventions are required with regard to the input of identifiers. more...

Enter coordinates for a subrange of the query sequence. The BLAST search will apply only to the residues in the range. Sequence coordinates are from 1 to the sequence length.The range includes the residue at the To coordinate. more...

 
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Use the browse button to upload a file from your local disk. The file may contain a single sequence or a list of sequences. The data may be either a list of database accession numbers, NCBI gi numbers, or sequences in FASTA format.


Enter a descriptive title for your BLAST search [?]

This title appears on all BLAST results and saved searches.

Enter Subject Sequence
Subject sequence(s) to be used for a BLAST search should be pasted in the text area. It automatically determines the format or the input. To allow this feature there are certain conventions required with regard to the input of identifiers. more...

Enter coordinates for a subrange of the subject sequence. The BLAST search will apply only to the residues in the range. Sequence coordinates are from 1 to the sequence length.The range includes the residue at the To coordinate. more...

 
[?]

Use the browse button to upload a file from your local disk. The file may contain a single sequence or a list of sequences. The data may be either a list of database accession numbers, NCBI gi numbers, or sequences in FASTA format.

Choose Search Set
Database sequences non-default value [?]

Select the sequence database to run searches against. No BLAST database contains all the sequences at NCBI. BLAST databases are organized by informational content (nr, RefSeq, etc.) or by sequencing technique (WGS, EST, etc.). more...

Add organism

Enter organism common name, binomial, or tax id. Only 20 top taxa will be shown. [?]

Start typing in the text box, then select your taxid. Use the "plus" button to add another organism or group, and the "exclude" checkbox to narrow the subset. The search will be restricted to the sequences in the database that correspond to your subset.

Create custom database
Enter an Entrez query to limit search [?]

You can use Entrez query syntax to search a subset of the selected BLAST database. This can be helpful to limit searches to molecule types, sequence lengths or to exclude organisms. more...

Algorithm parameters Note: Parameter values that differ from the default are highlighted in yellow and marked with sign
Scoring Parameters
Match/Mismatch Scores non-default value [?]

Reward and penalty for matching and mismatching bases. more...

Gap Costs non-default value [?]

Cost to create and extend a gap in an alignment. Linear costs are available only with megablast and are determined by the match/mismatch scores. more...