Detection of Integrative and Conjugative Elements in a Bacterial Genome

Question

[Optimist]

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.

1. Is it fine to use use Multi Fasta files of Contigs downloaded from FTP link of NCBI ?
2. 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)?
3. 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