Global vs local alignments: Illustration of global and local alignments demonstrating the ‘gappy’ quality of global alignments that can occur if sequences are insufficiently similar.
Global alignments, which attempt to align every residue in every sequence, are most useful when the sequences in the query set are similar and of roughly equal size (This does not mean global alignments cannot end in gaps). A general global alignment technique is the Needleman-Wunsch algorithm, which is based on dynamic programming.
Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context. The Smith-Waterman algorithm is a general local alignment method also based on dynamic programming. With sufficiently similar sequences, there is no difference between local and global alignments.
EST is known as Expressed Sequence Tag. It is a unique stretch of DNA within a coding region of a gene that is useful for identifying full length genes and serves as a landmark for mapping. EST is a sequence tagged site derived form cDNA. STS is a short segment of DNA which occurs but once in the genome and whose location and base sequence are known. STS’s are detectable by PCR.
