Hello all. I have sequenced gene by sanger's sequencing using both reverse and forward primer. I have made contig using Cromas pro then i have tried to removed vector contamination from using vec screen. In vec screen result when i am doing for reverse and forward sequence the vector sequence is present at ends, but with contig there is sequence after the vector sequence . so i want to know should i take only the sequence between the vector sequence form contig or i should include sequence after the vector. further when i am aligning vector removed sequence form forward and reverse complement of reverse primer and sequence from contig (only that sequence that is between vector and excluding that is after the vector), then forward and reverse are having similarity but there is no similarity with contig. I am also attaching the image of vec screen result.
Hi Saurabh, What is the size of your insert? Since you might have designed primers based on a known sequence you can check the sequence (in white) by a pairwise alignment with your known sequence.
Another point is you can blast the sequence after vector sequence to know if it hits to your required gene sequence.
Thanks Chakravarthi Mohan for your suggestion. Size of the insert is supposed to be about 350 bp and the sequence is showing similarity to the known sequence in pairwise alignment after vector removal. But I still want to know why this kind of dissimilarity is there in vec screen result .
- Badges
- Science topic
- Similar topics
- Computer Science and Engineering
- Bioinformatics
- Bioinformatic Tools