The program has many nice features and is easy to use once you have played around with it for a while.

Tr '() ' '()*' /Desktop/masters_repeats/anolis_repeatfamily_3way_total_oneline. BioEdit by Tom Hall is a very useful sequence editing program for PC users who work on a budget. #i have to make all the entries one line, so i replaced the newline with a * #concatenate all the files from all 3 species into one sub-subfamily specific fileĬat species1.fasta species2.fasta species3.fasta > /Desktop/masters_repeats/anolis_repeatfamily_3way_total.fasta I had to do some Googling to find the appropriate bash commands, to process the fasta files from the terminal command line.ġ) cat - concatenated all the files into 1 large fileĢ) I want to sort by line size, but if you do it with a normal fasta file, the header is read as a different line than the sequence body (so it'll delete all the sequences under 250 INCLUDING the fasta headers, which have all the information I need!) Therefore, I had to remove all newlines and put in a * so the header and sequence all are read as one long line.ģ) Next I used awk to sort based on size and I removed all sequences that are less than 250 base pairs.Ĥ) Put the fasta format back the way it was before I sorted based on size. One challenge I face is moving the data around and formatting it properly. Several sequence manipulation and analysis options and links to external analysis programs facilitate a working environment. All 3 of these genomes are Illumina Next-Gen. BioEdit is a free biological sequence alignment editor with an intuitive multiple document interface with convenient features designed to make alignment and manipulation of sequences relatively easy on desktop computers. I am doing a 3 way comparison of repeat elements in 3 species of anole lizards.

How to master sequence bioedit