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Enter one or more queries in the top text box and one or more subject sequences in the lower text box. Then use the BLAST button at the bottom of the page to align your sequences. To get the CDS annotation in the output, use only the NCBI accession or gi number for either the query or subject.
- Protein Blast
PSI-BLAST allows the user to build a PSSM (position-specific...
- Tblastn
PSI-BLAST allows the user to build a PSSM (position-specific...
- NCBI Blast
We would like to show you a description here but the site...
- Protein Blast
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.
From the BLAST mini-course page, click on the link “Align two sequences (bl2seq)” in the panel labeled “Special.” Paste the query nucleotide sequence from the problem in the box for Sequence 1 and the accession number, AF482979, in the second box.
) Enter query and subject sequences and select “BLAST”: ) View standard BLAST report. “Dot Matrix view” is available if there was only one subject sequence:
“Align Two Sequences” uses BLAST formatter to display search results. This makes the following possible: displaying the alignment in more formats (A, D), such as “Pairwise with identities”; downloading alignment (B) in XML, plain text, Hit table and comma delimited format for future reference;
Within the alignments section: Each alignment with a score > threshold (up to limit defined) is shown. The sequence listed is the one which matched the query sequence. In the red box are shown the Score, Expect value, Identities, Gaps and which strands of the query and database sequence aligned.
Starting from the query sequence column on the left and cross-referencing to the right, a user will arrive at the specific BLAST program(s) best suited for that search. This document is also available in PDF (163,516 bytes).
