Align sequences and run BLAST

Use pairwise alignment for two sequences, multiple alignment for a set of clones, and BLAST to identify an unknown sequence.

Compare two sequences

1. Open a plasmid. Run Compare / Align Sequences from the Tools panel or Ctrl/Cmd+K.
2. In Pairwise Alignment, fill Reference and Query. Paste FASTA or raw sequence, or pick a plasmid.
3. Choose a Mode: Global (end to end), Local (best region) or Semi-global (ends free).
4. Click Align.

Align many sequences

1. Run Multiple Sequence Alignment from the Tools panel or Ctrl/Cmd+K.
2. Tick the plasmids and sequencing reads to align. Use Filter sequences… to narrow the list.
3. Pick the Engine. An engine that is not installed shows as unavailable.
4. Pick the Reference. By default, differences are reported against the first selection.
5. Choose a project to save into. Alignments always go into a project.
6. Click Align.

Each difference is reported with the feature it lands in and whether it shifts the reading frame. Click History to reopen past alignments.

BLAST a plasmid or a selection

1. Open the plasmid. Run BLAST this plasmid, or right-click a selection or feature and choose Run NCBI BLAST.
2. Set Program, Database and Max Hits.
3. Click Run BLAST.
4. Pick a hit to see its alignment. Use Add to map to annotate the matched range, or Align with Query for the full alignment.
5. Click Save to Library to keep results as a CSV, or Export to download one.

BLAST a sequence from a file

1. In the Library, press Ctrl/Cmd+K and run BLAST from file....
2. Drop a FASTA file. If it holds several sequences, pick one and click Run BLAST on selected.

Programs and databases

• Programs: BLASTn, BLASTp, BLASTx, tBLASTn and tBLASTx.
• Databases: Nucleotide (nt), Non-redundant (nr), RefSeq RNA, RefSeq Genomic and SwissProt.
• Pick a protein database (nr, SwissProt) for BLASTp and BLASTx. Pick a nucleotide database for the others.