To start a new Blast2GO project you just have to load your sequence data from a file into Blast2GO.
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 for the FASTA format:
>gi|121664|sp|P00435|GSHC BOVIN GLUTATHIONE PEROXIDASE MCAAQRSAAALAAAAPRTVYAFSARPLAGGEPFNLSSLRGKVLLIENVASLUGTTVRDYTQMND LQRLGPRGLVVLGFPCNQFGHQENAKNEEILNCLKYVRPGGGF
Once the sequences have been loaded to Blast2GO, 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.
Figure 1: Context Menu: Show Sequence
Sequence Length Statistics
Blast2GO allows you to visualise the length distribution of your sequences in the arrow next to the "Chart'' icon.
Add sequences to existing Blast2GO project
Use the File Manager context menu to merge to project. Select two or more project, open the context menu with a right click on one of the files and select Merge.
In case one of your existing files is in .dat format just open it by selecting the file-type in File > Load Project (.dat Legacy Format). If the loaded project file has only Blast results and no sequence information it is still possible to add the corresponding sequences to Blast2GO 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 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 Blast2GO (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.
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