Map Features

The Map Features template, located in the Templates panel, lets you map chosen annotations from a source sequence to a target sequence using some of the same alignment algorithms used by MegAlign Pro. In cases where an input file contains more than one sequence (e.g., multiple chromosomes), only one sequence may be used at a time.

The Map Features template consists of a multi-screen wizard consisting of the Feature, Sequences, Options and Output screens. To navigate between the four wizard screens, either use the Back or Next buttons or click on the screen name in the left panel of the wizard.

The following are some scenarios where the Map Features template may be useful:

• You have two closely-related sequences, but one has missing annotations. With Map Features, you can map the desired annotations from the “complete” sequence to the “incomplete” one.

• You have a file containing features for the source sequence. With Map Features you can map the desired features to a second, closely-related, sequence.

• You want to map features from an old, annotated version of a sequence to a new, unannotated version.

SeqNinja can read from and write to a variety of source files, including FASTA (.fas, .fap, .fasta), GenBank (.gbk), DNASTAR Lasergene DNA and protein sequence files (.seq, .pro), DNASTAR Star Feature Files (.starff), and Variant Call Format files (.vcf). SeqNinja automatically recognizes the format of a source file by its extension.

*Note: If you wish to save to VCF format, you must use a VCF file as input.

A feature table may refer to chromosome sequences in any order and might contain a superset of sequences. SeqNinja automatically skips blocks of features for sequences that are not in the relevant sequence expression. For example, if you are only interested in chromosome 1, you can still use a VCF file containing variants for all the chromosomes.