The ARB Project
A free sequence database application for Unix. It includes a sequence editor, several sequence aligners, phylogeny reconstruction tools, probe/primer search and generation, genome annotation and visualization. In addition to the integrated user-interface the ARB database can be accessed using Perl or C.
http://www.arb-home.de

Linear Complexity: A Literature Survey
The linear complexity (LC) of a sequence is the size in bits of the shortest linear feedback shift register (LFSR) which can produce that sequence. The measure speaks to the difficulty of generating, and perhaps analyzing, a particular sequence.
http://www.ciphersbyritter.com/RES/LINCOMPL.HTM

Transcription
Wikipedia article: in genetics the process by which a DNA sequence is converted to a corresponding RNA sequence.
http://en.wikipedia.org/wiki/Transcription_%28genetics%29

Antibodies - Structure and Sequence
Attempts to summarize useful information on antibody structure and sequence. Provides a query interface to the Kabat antibody sequence data, general information on antibodies and crystal structures, and links.
http://www.bioinf.org.uk/abs/

HIV Sequence Database
The HIV Databases cover HIV sequences, HIV molecular immunology, HIV drug resistance mutations and nonhuman primate HIV/SIV vaccine trials. Each of these topics are available through a dedicated database, extensively annotated and with many specialized search and analysis tools. The HIV databases are supported by the NIH and DOE and maintained at the Los Alamos National Laboratory.
http://www.hiv.lanl.gov/content/index

Translation
Wikipedia article: in genetics, the process by which ribosomes in the cytoplasm transfer the genetic code from a m-RNA sequence to an amino acid sequence in a polypeptide chain.
http://en.wikipedia.org/wiki/Translation_%28genetics%29

AlgoNomics
Provides online, as well as on-site, tools for protein sequence analysis and structure prediction. Focused on the relationship between the amino acid sequence of proteins and their function.
http://www.algonomics.com

3D-PSSM Fold Recognition
Combines sequence and structural information for predicting the structure and/or function of your protein sequence, and can detect remote homologies beyond PSI-Blast.
http://www.sbg.bio.ic.ac.uk/~3dpssm/

Sequence V1.5
Sequence V1.5 is a program for sequencing linear or cyclic peptides from combinatorial split-and-pool libraries using collision induced dissociation mass spectrometry.
http://www.kombyonyx.com

On-Line Encyclopedia of Integer Sequences
Identify a sequence by entering few terms in the sequence. Additional information includes examples, formulas, and related links.
http://www.research.att.com/~njas/sequences/