Sequences

Content of this page:

To start a new OmicsBox project for the Functional Analysis you just have to load your sequence data from a file into OmicsBox.

Load sequences from start

At the "File'' menu, go to Load > Load Sequences > Load Fasta File and select the file containing your sequences. The application accepts text files containing one or more DNA or protein sequences in FASTA or FASTQ format (see below). These files must have the extension .fasta,.fnn,.faa,.fna,.ffn.txt.fq or .fastq to be accepted by the application.

A sequence in FASTA format begins with a single-line description or header starting with a ">'' character. The rest of the header line is arbitrary but should be informative. Subsequent lines contain the sequence, one character per residue. Lines can have different lengths. Be sure your file is in this format and avoid strange characters in the sequence header, such as '&' or '\' and use 'N' to denote in-determinations in the sequences.

An example of the FASTA format:

>gi|121664|sp|P00435|GSHC BOVIN GLUTATHIONE PEROXIDASE
MCAAQRSAAALAAAAPRTVYAFSARPLAGGEPFNLSSLRGKVLLIENVASLUGTTVRDYTQMND
LQRLGPRGLVVLGFPCNQFGHQENAKNEEILNCLKYVRPGGGF

Show Sequence

Once the sequences have been loaded to OmicsBox, it is possible to see them by right-clicking on the Sequence Table. The "Single Sequence Menu'' (context menu) will appear (figure 1). This menu provides some functions for sequences individually, i.e. will apply to the sequence at that position of the Table.
With the sequence viewer, it is possible to copy the sequence to the clipboard.

Image showsequence

Figure 1: Context Menu:  Show Sequence

Figure 2: Sequence Viewer

Sequence Length Statistics

OmicsBox allows you to visualize the length distribution of your sequences in the arrow next to the "Chart'' icon.

Add sequences to existing OmicsBox project

Use the File Manager context menu to merge into the project. Select two or more project, open the context menu with a right click on one of the files and select Merge.

In case the loaded project file has only Blast results and no sequence information it is still possible to add the corresponding sequences to OmicsBox project by clicking on the arrow next to the "Start'' icon and select "Load Sequences''. Now two options will be displayed "Create new project'' see figure 3 and 4, and "Add to the existing project''. The "Add to the existing project'' option should be selected and in the next page, you can browse for the fasta file and "Overwrite'' option should be selected. 



Figure 3: Load Sequences Dialog: Add sequences to an existing project


Figure 4: Load Sequences Dialog: Choose Fasta file


Export FASTA Sequence with Annotation Results

After executing the whole functional annotation of the sequences in OmicsBox (BLAST, Mapping and Annotation) it is possible to export the sequence in FASTA format with the corresponding sequence description and GO ID or GO term from File > Export > Export as FASTA.

An example of the Exported FASTA format with Sequence Description and GO IDs: 

>C04018C10|mitogen-activated protein kinase 3|GO:0005634;GO:0004707;GO:0005515
acaaacgagagcgtagaaaattaattagagagaaaaagagagagagtaaaatggctgacgtggcgcaggtcaacg
gcgtaggtcaaacggctgattttcctgcggtaccgacgcacggcggtcagtttatacagtacaatatatttggaa
acttgtttgaaatcacggccaagtatcggcctccgatcatgccgattggtcgcggcgcgtacgggatcgtttgct
cggtgttgaatacggagacgaatgagctcgttgcgatgaagaaaatagcgaacgcttttgataatcacatggatg
ccaagcgaacgcttcgtgagattaagcttctgcaacatttcgatcatgaaaatgtgatagctgtaaaagatgtgg
ttcccccaccgttacgaagagaattcactgatgtctatattgctgcggaactcatggacactgacctttaccaaa
ttattcgctcaaatcaaagtttatccgaggagcactgccagtatttcttgtatcaacttcttcgaggactcaagt
atatccattcagcaaatgttattcatcgggatttgaagcccagcaatctcttgttaaatgcaaattgtgatttaa
aaatttgtgattttggtcttgctcgtccaacctcggagaatgagttcatgacagagtatgttgtcacaagatggt
accgagcccctgagttgttattgaactcatctgactacactg