Hi Folks !!
I'm working on the pathogenomics of MDR bacteria involving extensive Genomic analyses. As part of this project I need your inputs & clarifications on the detection of Integrative and Conjugative Elements (ICEs) in my genome. Queries are listed below.
- Is it fine to use use Multi Fasta files of Contigs downloaded from FTP link of NCBI ?
- Should I remove headers of all the contigs (167 in my case) and stitch them up to form a single line of string (utilization of sequence massager or even MAUVE)?
- What are the tools that can be involved in ascertaining the presence of ICEs in my genome along with annotations?
Please help me with tools (web based, command-line based, Linux packages, R Packages) & Literature source that can be used for the above said purpose.
Thanks a lot for the help & support