A collection of online tools that help us in designing and research analysis

Protein and Gene database search
Protein: http://www.ncbi.nlm.nih.gov/protein       
DNA: http://www.ncbi.nlm.nih.gov/nuccore/
Used to find protein and DNA sequences in nature that match your description i.e Blue proteins, fluorescent proteins, ethanol proteins, salt-tolerance conferring proteins.

Protein sequence finder
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins
Finds other proteins in nature that are similar to the protein sequence you input to find evolutionary homologies, similar functions or possible alternatives to your protein etc.

Protein sequence comparer
https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&BLAST_SPEC=blast2seq&LINK_LOC=blasttab
Highlights similarities between two protein sequences of your choice to identify similar structural motifs and common regions.

DNA to Protein converter
http://web.expasy.org/translate/
Used to convert your DNA sequence to an amino acid sequence, which is then used for sequence comparison or analysis

Updates: Added 'Online tools' section