You can use the Folder Sequence Query dialog box to filter results and display the following:
- a text file describing the analysis
- a horizontal map displaying the aligned sequences represented as horizontal bars
- an aligned sequence display.
1. The Folder Sequence Query display dialog box is displayed on completion of each analysis. To display this dialog box at other times, for example to change the display parameters, choose Database | Align to Folder when any analysis display result window is active.
2. You can limit the displays to a single match or to a consecutive subset of the ordered matches by typing the numbers in the Entries to show text boxes.
3. You can limit the region that will be scored by typing in the numbers that bracket the region in the Score Rgn text boxes, or by selecting a region from the features table drop-down menu that appears to the right of the text boxes.
The numbers are with reference to the query sequence.
4. You can limit the region that will be displayed by typing in the numbers that bracket the region in the Display Rgn text boxes, or by selecting a region from the features table drop-down menu that appears to the right of the text boxes. The numbers are with reference to the query sequence. The display region must lie within the score region.
5. Select Description list to display a list of the saved matches in order of optimized score.
6. Select Horizontal map to display a graphical representation of the alignments.
7. Select Aligned sequences to display the optimized alignments between the query sequence and each of the saved matching sequences.
8. Select OK to generate the results displays.
The Horizontal Map window shows the aligned sequences with scores. Vertical lines through a sequence represent residues ignored to optimize a score; white space represents gaps inserted to optimize scores.
The Description list shows the locus name of the sequence, its optimized and initial scores, and the first part of the sequence entry's definition line, if one was present.
The Aligned Sequence window shows the residue-by-residue comparison of each aligned sequence with the query sequence. The exact appearance of this window is controlled by options on the Aligned Formats dialog box, accessed by Options | Format Aligned Display.
For any sequence in the folder, only one match can be reported. If a folder sequence yields more than one match to the query sequence, only the best match is shown in the results window.
When searching a user folder, there are certain very rare situations that would cause MacVector to treat some protein sequence files in the folder as if they were nucleic acid sequences and vice versa. This is due to the way that MacVector differentiates sequence types. If a sequence file contains no information about the type of molecule present (this occurs with line or old-format GCG files), MacVector attempts to classify the sequence by counting the number of A, C, G, T, and U characters and non-printing ASCII characters in the first line of the sequence data. If any non-printing ASCII characters (null characters or control characters) are found in the first line of the sequence data, MacVector assumes that the file is not a sequence file and will not attempt to compare it to the query sequence. If there are no non-printing characters, it checks to see if the count of ACGTU characters exceeds 90 percent of the total characters in the line. If so, the sequence is assumed to be a nucleic acid sequence. Otherwise it is considered to be a protein sequence. If any of the protein sequences in the user folder you are searching are line or GCG files, and have an unusual amino acid composition (abnormally rich in alanine, cysteine, glycine, or threonine), they may be mis-tagged as nucleic acid sequences. Alternatively, if there are any nucleic acid sequences present that contain an unusually high percentage of ambiguous base assignments in the first part of the sequence, they may be misclassified as protein sequences and thus not compared with the query sequence. Such misclassifications will probably occur only for very short sequences with unusual compositions.