images

Mulder and other biochemists in the 1830s and 1840s hypothesized that all proteins had the same composition of carbon, hydrogen, nitrogen, oxygen, phosphorus, and sulfur. Simon (1846) summarized the composition of known proteins, including fibrin, casein, crystalline, and pepsin. He noted that the composition of globulin (i.e., hemoglobin) was not yet known.

5

images

Advanced Database Searching

INTRODUCTION

In Chapters 3 and 4 we introduced pairwise alignments and BLAST searching. BLAST searching allows one to search a database to find what proteins or genes are present. BLAST searches can be very versatile, and in this chapter we will cover several advanced database searching techniques.

Using human myoglobin (NP_005359) as a query in a blastp result against human RefSeq proteins, beta globin does not appear.

Let us introduce two problems for which the five main NCBI BLAST programs are not sufficient. (1) We know that myoglobin is homologous to alpha globin and beta globin; all are vertebrate members of a globin superfamily. We have seen in Fig. 3.1 that myoglobin shares a very similar three-dimensional structure with alpha and beta globin. However, if you use beta globin (NP_000509) as a query and perform a blastp search (restricting the output to human and setting the database to nr ...

Get Bioinformatics and Functional Genomics, Second Edition now with O’Reilly online learning.

O’Reilly members experience live online training, plus books, videos, and digital content from 200+ publishers.