# Building custom cry Hidden Markov model
# jk2739
# 04/21/16

# 1 - Download following cry sequences from NCBI:
# gi|751813701
# gi|14486714
# gi|378947603
# gi|17977981
# gi|161598576
# gi|161598618
# gi|8927991
# gi|228809514
# gi|228841405
# gi|8469164

# 2 - Align cry sequences using MUSCLE (default settings, MEGA6.06)

# 3 - Build Hidden Markov Model based on the alignment (HMMER v3.1b2)
hmmbuild cry.hmm cry_aligned.fasta

# 4 - Translate WGS in 6 ORFs (EMBOSS v6.5.7)
transeq -sequence <WGS_contigs.fasta> -outseq <WGS_contigs_translated.fasta> -frame 6 -clean

# 5 - Concatenate translated genomes
cat *_translated.fasta > wgs_db.fasta

# 6 - Search for cry genes in translated wgs sequences(HMMER v3.1b2)
hmmsearch cry.hmm wgs_db.fasta > cryhmm.out

# 7 - Determine the treshold for positive hits based on bitscores for 10 sequences used for building the cry.hmm
hmmsearch cry.hmm cry_aligned.fas > cryhmm_treshold.out