/data/users/gbalderr/ncbi-blast-2.7.1+/bin/blastx -query Transcripts.fa -db landmarkdb/landmark -out 1.xml -evalue 0.001 -outfmt 5 -num_threads 32
The xml output files generated by BLAST were the input to get the annotation with BLAST2Go a functional annotation tool
We used exonerate to map mouse protein coding genes to the peromyscus genome in order to compare mouse domain prevalence with maximum sensitivity. We predicted the Peromyscus proteome using TransDecoder on on the longest isoform per exonerate gene model and predicted protein domains using the PFAM database v.31(https://pfam.xfam.org/) and HMMR 3.1b2 (http://hmmer.org/) run with default settings and profile reporting threshold of 1e -06. We also did the PFAM analysis on the mouse proteome (GRCm38) with the same parameters.
After obtaining the AA squencences we had to modify the headers to get rid of the patterns and be able to get rid of duplicates
sed 's/.t*.g* ---NA---/ /g' Protein_seq_Peromyscus.fasta > Protein_A.fasta
sed 's/.t../ /' Protein_A.fasta > Protein_B.fasta
Then I used an script I found in Github a script Keep-longest.py to remove duplicates by keep the longest sequence And my version can be found in
python removedup.py Protein_B.fasta > Peromyscus_Protein.fasta
We downloaded the PFam database PFam-A.hmm, so we could match our sequences with the domains. The original script can be found here
module load hmmer/3.1b2
hmmscan -E 0.000001 --domE 0.001 --tblout Peromyscus.table.txt --domtblout Peromyscus.domains.txt --noali --cpu 32 Pfam-A.hmm /share/samdata/gbalderr/peromyscus/blast/Peromyscus_Protein.fasta
We used RepeatMasker version opne-4.0.7 (http://repeatmasker.org/) on the Peromyscus, mouse (GRCm38) and rabbit (OryCun2.0) genomes to annotate interspersed repeats and low complexity DNA sequences. The search engine used was NCBI/RMBLASTE (2.2.23+) in combination with the option -mammal for indicating the database to be used.
module load mchakrab/repeatmodeler/1.0.11 module load mchakrab/repeatmasker/4.0.7
RepeatMasker -pa 8 -xsmall -gff -s --species mammal -dir RMoutGBG -e ncbi peromyscus_assembly_scaffolds.fasta
