Dfam

[…] by using translated RefSeq viral genomic sequences (). To confirm the identity of retrotransposons, NHHMER was used to align nucleotide query sequences against profiles in the Repetitive DNA Element (DFAM) database v1.4 (). For BLASTX and PFAM analyses, DNA query sequences were translated to protein sequences in all six reading frames. Finally, nucleotide sequences without significant BLASTN hits […]

[…] programs: RepeatMasker, RepeatScout [], RECON [] and TRF (Tandem Repeat Finder) []. RepeatMasker identifies and masks interspersed repeats using curated libraries of consensus sequences supported by Dfam; Dfam contains entries corresponding to all Repbase TE entries, and each Dfam entry is represented by a profile hidden Markov model. RECON evaluates pair-wise similarities to build repeat consens […]

[…] e TEs . One of the best known is RepeatMasker, which harnesses nhmmer, cross_match, ABBlast/WUBlast, RMBlast and Decypher as search engines and uses curated libraries of repeats, currently supporting Dfam (profile HMM library) and Repbase , .Another important tool is the REPET package, one of the most used tools for large eukaryotic genomes with more than 50 genomes analyzed in the framework of in […]

[…] the AUGUSTUS package [] with the initial model “human” (H. sapiens) was used (Additional file ). The masking was performed with the RepeatMasker package [] using the RepBase repeats libraries [] and Dfam []. Annotation was carried out with scripts based on the funannotate pipeline [].The protein and transcriptomic hints for marking the position of genes were also used. Protein hints were obtained […]

[…] the 406 individuals with nasal polyps, 350 were index patients with CRSwNP, 22 of the non-index patients knew they had polyps beforehand and 34 had newly discovered polyps.The Manhattan plot from the DFAM analysis is provided in and the Manhattan plot from the EMMAX analysis in . lists the 30 SNPs with the strongest associations from the DFAM analysis and lists the 30 SNPs with the strongest as […]

[…] Consensus sequences for elements for up-regulated TEs were downloaded from the Dfam database (). Stranded RNA-seq data were then aligned to consensus sequences using BWA-MEM and quantified using HTseq-count (; ). Reads were visualized using the Integrative Genomics Viewer (IGV) […]