| List of Programs Used in the Tutorial | ||
|---|---|---|
| Task | Program and Instructions | Output |
| Define region to analyze and get sequences | 1. FASTA-formatted sequence files, one for each of the species that you are comparing 2. Accession numbers for each of the mRNA sequences encoded in the genomic sequence (base organism only) |
|
| Compare mRNA sequences with genomic fragment to identify exons | Table of exon boundaries using the numbering of your genomic sequence | |
| Make an annotation file | Vi, TextEdit, SimpleText, Notepad, or any other text-processing program; if necessary, use Word or WordPerfect or another word-processing program, saving the annotation file as text | Text-formatted annotation file |
| Compare sequences using VISTA | 1. E-mail message with link to VISTA directory; 2. Plot, in Portable Document Format (PDF; open with Acrobat, Ghostscript or Preview) 3. List of aligned regions 4. Aligned sequences (This will be a huge file) 5. Copies of the original sequences 6. Copies of the original sequences with repeats changed to N's (for use in other programs) 7. List of repeats found |
|
| Compare sequences using PipMaker | E-mail message with output files attached; file formats as for VISTA | |
| Find sequences in organisms without fully sequenced genomes | FASTA-formatted sequence files | |
| Mask repetitive sequences (This task needs to be done before sequences are compared with PipMaker) | E-mail message with list of repeats | |
| < | Start | Get Sequences | ID Exons | Annotate | VISTA | PipMaker | References | > |
