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seq files store sequence information in a text format called FASTA.

In FASTA format, each sequence starts with a line containing a greater-than sign (>) and a descriptive header (this is the name of the sequence). The name of the sequence is added without introducing a space. The following image shows the forward and reverse sequence of the “TutorialExample” in FASTA format. The “>” sign is highlighted in pink, the descriptive header is shown in blue and the sequence is depicted in brown. To be able to align the forward and reverse sequence reads, the two sequences have to have the same orientation. This can be achieved by converting the reverse sequence read into its reverse complement (i.e. converting the 3′-5′ sequence into a 5′-3′ orientation). The example below illustrates the principle of reverse-complementing a reverse read. The following steps are carried out in order to convert the reverse sequence read into its reverse complement:ġ.

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Seq file of your reverse sequence using a text editor such as NotePad on Windows or TextEdit on Mac. seq file contains the sequence information in FASTA format.Ģ. Copy the whole sequence including the “>” sign and descriptive header (keyboard shortcut Ctrl + C).ģ. Paste all the information into the EMBOSS Seqret input box below (Ctrl + V). Alternatively, use the upload function to upload the reverse. In “Step 1” ensure “DNA” is selected as input data. In “Step 2” select “FASTA format” as input and output format. To receive the reverse complement of the sequence, click on “More options” and select “Yes” as “Reverse” option. To view the EMBOSS Seqret search window containing “TutorialExample” sequence and correct parameter settings click here.Ħ. Open an empty text editor document on your computer.ħ. Once your reverse complement sequence is available in the “Tool Output” window of EMBOSS Seqret, copy the whole sequence into the new text editor document (Ctrl + C and Ctrl + V). Again, include the “>” sign and descriptive header when copying the sequence. To view the EMBOSS Seqret results window showing the “TutorialExample” sequence in reverse complement click here.Ĩ.

Keep the “>” sign at the beginning sequence information but replace the descriptive header by “SampleID_RP_RevComp”. Save the new text editor document as “SampleID_RP_RevComp” on your desktop.

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