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AlignIR Software

Extensive File Compatibility

A fully functional demonstration edition of AlignIR is available upon request from LI-COR or your LI-COR distributor.

Compatible Input File Types

  • LI-COR sample files
  • LI-COR curve files
  • Sequence (text) files from any source
  • FASTA and Genbank text files
  • Curve files from other automated sequencers

Automatic Alignments

AlignIR Automatic Alignments
  • After creating an AlignIR project and importing your files, you can use the automatic alignment software to produce a consensus that is ready for detailed examination.
  • The consensus can be calculated using either a weighted or minimum method. The weighted method uses the base letter with the highest count as the consensus call. The minimum method takes all base letters into account and generates an IUPAC ambiguity code for combinations of bases at that position.
  • The consensus sequence is shown in a row below the last sample sequence.
  • The Annotation row makes it easy to see ambiguities and mismatches in the consensus sequence.
  • A variety of color schemes can be used in the AlignIR window to highlight sequence differences.

Sequence Assembly

  • Vector Removal: Before vectors are actually trimmed, a report is displayed listing the vector sequences that will be trimmed from each sample. Vector matching parameters give you a fine degree of control over finding and removing vector sequences.
  • Samples that have been reverse complemented during assembly are shown with their names in a different color(red in the image - Figure 1).
  • An overview window can be opened that displays a high level overview of the contigs in your project.
  • The overview shows the consensus sequence as colored bars with overlapping samples shown as black horizontal bars. Forward samples are displayed above the consensus and reversed samples are shown below (Figure 3).
  • Each contig is saved in a different file. Contig files can be imported into new projects as if they were a sample file, which helps break large projects into smaller modules.
  • Sequence data for any contig can be displayed in the main AlignIR window for editing or sequence verification.
AlignIR sequence assembly 1

Figure 1

AlignIR sequence assembly 2

Figure 2

AlignIR sequence assembly 3

Figure 3

Powerful Editing

AlignIR powerful editing 1

Figure 1

  • Whether your project is an assembly or an alignment, your raw data is always linked to the sequence data in the AlignIR window. To open a sample file for editing or verification, you simply double click on the sequence in the AlignIR window.
  • Edit windows for LI-COR sample files feature side-by-side display of image and curve data for high accuracy editing Quality values (error probabilities) are also displayed in numeric or bar graph format (Figure 2). Samples with only curve data are shown in curve editor windows(center window - Figure 1).
  • Cursor positions between the AlignIR window and edit windows are synchronized to make editing even more powerful. Using one of AlignIR's navigation features like "go to next ambiguity" will result in all open editor windows automatically updating to the location of the next ambiguity in the consensus.
  • Edits to the sequence in the AlignIR window or in the curve/image edit windows are made by just highlighting the sequence and typing the appropriate base letter or IUPAC ambiguity code.
  • Both curves and images can be magnified to enhance editing.
AlignIR powerful editing 1

Figure 2

Search Functions

AlignIR search functions
  • AlignIR has three search modes to assure that you will quickly find the sequence you are looking for:
  • Best Match searches find exactly the sequence you enter, or something close to your sequence if you set the match percentage below 100%.
  • IUPAC Searches let you enter search strings containing IUPAC ambiguity codes. Using an IUPAC search, AlignIR will also find sequences that are the same as the sequence you enter except that an appropriate IUPAC ambiguity code has been inserted at some position.
  • Regular Expression Searches let you extend your search capabilities by adding expression operators to your search text. Expression operators can be "wild card" characters, logical operators like "and" or "or", and a variety of other operators that help you do things like finding repeat sequences with any number of repeats.

Multiple Reports

  • For the consensus sequence or single sample sequences, AlignIR produces reports in the following formats:
    • Sample Report Formats:
      • EMBL
      • FASTA
      • Genbank
      • Plain Text
      • GCG/RSF
      • IG/Stanford
      • PIR
  • Alignment Report formats include:
    • Alignment Report Formats:
      • LI-COR: HTML
      • MSF/RSF
      • Phylip

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