BLAST

This is the Title of the Book, eMatter Edition

Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.

14

|

Chapter 1: Hello BLAST

The other available alignment options allow a multiple sequence alignment view of

the BLAST hits. One of these multiple alignment options, query-anchored with iden-

tities, is shown in Figure 1-14. In this view, the full sequence of the query is shown

on the top line with a unique identifier (1_18852, in this case). Subsequently, each

line shows the alignment for one database hit. Identical residues are represented with

a dot (.), while nucleotide differences are shown explicitly. This alignment option is

useful for quickly identifying changes common to a group of sequences. For exam-

ple, you can see from the part of the alignment shown in Figure 1-14 that the bot-

tom four sequences (6754225, 664837, 664835, and 664831) have common shared

differences. A deeper look into these sequences reveals that they are actually differ-

ent database entries for the same mouse Hoxa11 gene, which is homologous to the

coelacanth Hoxa11 gene.

The other multiple sequence alignment views are similar to this one, but differ on

whether or not they show identical residues (with or without identities) and whether

the gaps are displayed in the query sequence or in the subjects (flat or not). You’ll

find a detailed explanation of these alignment options in Appendix A.

The Next Step

This chapter has taken you through a simple BLASTN search at the NCBI database;

however, more than two dozen specialized BLAST pages are available, and they let

you do anything—from screening for vector sequence, to identifying protein family

Figure 1-14. Query-anchored with identities view