Sequence and Structural Databases

TBLASTN queries protein sequences to a nucleotide sequence database with the sequences translated in all six reading frames.

Comparative sequence analysis is the first step to study sequence-structure-function relationship in protein and nucleotide sequences. E.g: 
Protein sequences: Blastp, PSI-BLAST and PHI-BLAST
Nucleotide sequences: MEGABLAST, Discontigous-megablast and Blastn

This option is correct because probably the most well-known progressive alignment program is Clustal. Clustal is a progressive multiple alignment program available either as a stand-alone or on-line program.
Poa (Partial order alignments) is a progressive alignment program that does not rely on guide trees. Instead, the multiple alignment is assembled by adding sequences in the order they are given.

FirstEF is a web-based program that predicts promoters for human DNA.

The Readseq program is able to perform format conversion of multiple alignments. Readseq is a web-based program that is able to do both simple sequence format conversions as well as alignment format conversions.

CpGProD is a web-based program that predicts promoters containing a high density of CpG islands in mammalian genomic sequences.

This option is correct because PROSITE is a protein database consisting of entries describing the protein families, domains and functional sites as well as amino acid patterns and profiles in them and VectorBase is an NIAID Bioinformatics Resource Center dedicated to providing data to the scientific community for Invertebrate Vectors of Human Pathogens.

This option is correct because UniProt is a comprehensive, high-quality and freely accessible database of protein sequence and functional information. InterPro is a database of protein families, domains and functional sites in which identifiable features found in known proteins can be applied to new protein sequences in order to functionally characterise them. The Structural Classification of Proteins (SCOP) database is a largely manual classification of protein structural domains based on similarities of their structures and amino acid sequences. ModBase is a database of annotated comparative protein structure models, containing models for more than 3.8 million unique protein sequences.

Comparative Toxicogenomics Database (CTD) describes relationships between chemicals, genes and human diseases. CTD promotes understanding about the effects of environmental chemicals on human health by integrating data from curated scientific literature to describe chemical interactions with genes and proteins and associations between diseases and chemicals and diseases and genes/proteins.

This option is correct because NetPath is a manually curated resource of human signal transduction pathways and Reactome is a navigable map of human biological pathways, ranging from metabolic processes (metabolic pathways) to hormonal signalling (signal transduction pathways).

TreeFam is a database of phylogenetic trees of animal genes which aims at developing a curated resource that gives reliable information about ortholog and paralog assignments and evolutionary history of various gene families.

SILVA is a comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data.

Kyoto Encyclopedia of Genes and Genomes (KEGG) is a collection of online databases dealing with genomes, enzymatic pathways and biological chemicals.

CAZy is a database of Carbohydrate-Active enzymes, which contains classification and associated information about enyzmes involved in the synthesis, metabolism and transport of carbohydrates.

MEDLARS Online is a bibliographic database of life sciences and biomedical information which provides bibliographic information for articles from academic journals covering medicine, nursing, pharmacy, dentistry, veterinary medicine, and health care.
DNA Data Bank of Japan (DDBJ) is a nucleotide sequence database. It is a biological database that collects DNA sequences.
NatureServe, Inc. is a sophisticated biodiversity database which acts as an authoritative source for information on more than 70,000 plants, animals, and ecosystems of the United States and Canada.
WormBase is an online biological database about the biology and genome of the model organism Caenorhabditis elegans (a nematode) and contains information about other related nematodes.