relationship among peptide functions, respectively; (iii) it is able to stably detect the newly detected therapeutic peptide functions with limited labeled data by introducing the MCRT algorithm; and (iv) its web server is constructed, only requiring the peptide sequences in FASTA format as inputs...
Contigs below 2.5 kbp were removed using anvi-script-reformat-fasta within anvi’o v6.2 [112]. Metagenome-assembled genome (MAG) retrieval and analysisMAG retrieval was performed as described previously [43] (Additional file 3). MAGs were classified into low-, medium-, and high-quality ...
NnWOX1-1-, NnWOX4-3-, and NnWOX5-1-encoded proteins were selected, standardized to fasta format, and then successively imported into the software channels. In the option section, each sequence marked by black color was set to represent homology. A phylogenetic tree was constructed using DNA...
The input folder requires microbial genome sequences in FASTA format and an optional set of genomic/metagenomic reads which were used to reconstruct those genomes (Fig. 1). The annotated proteins from input genomic sequences are queried against HMM databases (KEGG KOfam, Pfam, TIGRfam, and ...
as we are currently unable to generate an accurate and comprehensive catalog of the human transcriptome4. Although advances in high-throughput sequencing have enabled mapping of local elements (e.g., individual splice junctions), how these elements combine to form full-length isoforms is largely unk...
(http://ftp.ensembl.org/pub/release-106/fasta/gallus_gallus/dna) using BWA version 0.7.15 with the command ‘mem -t 10 -k 32’ [62]. Then, the BAM alignment files were generated from the obtained SAM format files using SAMtools (version 1.3), following the command “rmdup” [63]. ...
Discovery of conserved regions from GenModels GenModels provide vital information about the similarity between segments in the form of quasi-alignments. This allows us to identify regions that are highly similar across multiple sequences. For sequences related by evolution, such as those from the sa...
data can be uploaded, pasted or given via URL and options selected using a simple online form. A limited set of the VEP’s most commonly used plugins is available to use via the web interface. Requests are processed by a resource management system on the Ensembl web servers to distribute ...
The polypeptide sequence(s) can be typed or pasted on screen using FASTA format. Despite supporting up to 100 characters for name entries, use of very long names is discouraged as it disturbs the visualization of the output. Sequence entries may not contain more than 2,000 residues and the ...
In all these cases, the genomic binding sites of cooperating TFs form well-defined rigidly spaced motif complexes, i.e. motif pairs with fixed relative orientation and spacing. This is in contrast to indirect cooperativity, i.e. fuzzily spaced co-binding of any TF pairs, which can be ...