I already have the sequences of a DNA, (PCR product), sequenced from the forward and reverse primers, so how can i generate a contig sequence by using the Bioedit ?
Dear Hafiz Muhammad Rizwan and Mohamed Lachheb
You can easily edit and contig the forward and reverse sequences in Bioedit software by using “cap contig assembly program”. Just follow the following steps:
1) Keep your both forward and reverse sequence in a single text file and save as “.fasta” format.
2) Now open the sequence in Bioedit.
3) Click on “Accessory applications” followed by “cap contig assembly program” (let it be default settings in the dialogue box) and click on the “Run application”.
4) A command prompt window will appear. Just close it and your job is done.
5) You could be able to see an output window where the third line from the top will be your contig sequence (contig-0). You can copy that sequence and go for downstream analyses like BLAST etc.
All the best
Hi Colleague
please do the following steps
1) Save the sequences in a txt file and import them.
2) If necessary, you can select the reverse sequence set the "reverse and complement" command (shift+control+R) if the sequences came from a forward and a reverse primer...
3) Click in: Accessory application > CAP contig assembler program... A window asking for the parameters "length of overlap" and "% of complementarity" will appear (the default are 20 nt and 85%)...
4) Click enter, and enter again (after a DOS window appear)...
After this steps, the contig will appear together with the sequences ina new window... You can select the first and the last nt and copy the entire contig...
Regrads
The previous answers are correct, but with BioEdit there is also web accessible programs such as ClustalV.
However, for contigs I use the Staden Package (free to researchers) where I can perform assembly and check the trace files.
- Badges
- Science method