Sequence analysis tools

1. BLAST

It is the main tool of NCBI to compare primary Protein or DNA sequence to other sequences in various databases.
2. HMMER

HMMER is used for searching sequence databases for sequence homologs, and for making sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
3. CLUSTAL OMEGA

Clustal Omega is a new multiple sequence alignment program that uses seeded guide trees and HMM profile-profile techniques to generate alignments between three or more sequences.
4. PROT PARAM : 

This is a tool which allows the computation of various physical and chemical parameters for a given protein in Uniprot or for a user entered protein sequence.