Bioinformatics: Databases and Sequence Analysis Tools

This option is correct because McPromoter is a web-based program that uses a neural network to make promoter predictions.

This option is correct because BLOSUM is a substitution matrix in which scores for each position are derived from observations of the frequencies of substitutions.

This option is correct because Melina is a web-based program that runs four individual motif-finding algorithms, MEME, GIBBS sampling, CONSENSUS, and Coresearch simultaneously.

This option is correct because FindTerm is used for searching bacterial ρ-independent termination signals located at the end of operons.

This option is correct because CONPRO is a web-based program that uses a consensus method to identify promoter elements for human DNA.

This option is correct because COG  is a protein family database based on phylogenetic classification.

Algorithms That Use Prealignment
This type of algorithm requires the user to provide a pairwise or multiple alignment as input. The sequence alignment can be obtained using standard alignment programs such as T-Coffee, PRRN, or Clustal.
RNAalifold is a program in the Vienna package. It uses a multiple sequence alignment as input to analyze covariation patterns on the sequences.

Consensus-based gene prediction programs
Because different prediction programs have different levels of sensitivity and specificity, it makes sense to combine results of multiple programs based on consensus.
GeneComber is a web server that combines HMMgene and GenScan prediction results.
DIGIT is another consensus-based web server. It uses prediction from three ab initio programs – FGENESH, GENSCAN, and HMMgene.

This option is correct because in bioinformatics, the BLOSUM matrix is a substitution matrix used for sequence alignment of proteins.

This option is correct because TBLASTN queries protein sequences to a nucleotide sequence database.

This option is correct because all are correctly matched.
PAM matrix was developed by Margaret Dayhoff in the 1970s.
BLOSUM matrices were first proposed by Henikoff and Henikoff for aligning protein sequences.
PSWM was introduced by American geneticist Gary Stormo and colleagues in 1982 as an alternative to consensus sequences.

This option is correct because Readseq is a web-based program that is able to do both simple sequence format conversion as well as alignment format conversions.

This option is correct because GENSCAN is a web- based program that makes predictions based on fifth-order HMMs.

This option is correct because InterPro is an integrated pattern database that integrates information from PROSITE, Pfam, PRINTS, ProDom  and SMART databases. 

Phylogenetic Footprinting–Based Method
The identification of conserved noncoding DNA elements that serve crucial functional roles is referred to as phylogenetic footprinting; the elements are called phylogenetic footprints. This type of method can apply to both prokaryotic and eukaryotic sequences.
ConSite is a web server that finds putative promoter elements by comparing two orthologous sequences.
PromH(W) is a web-based program that predicts regulatory sites by pair- wise sequence comparison.