View - ResearchGate

Estimating Protein Function Using Protein–Protein Relationships 111tool (BLAST) (10) sequence comparison approach. Users who find computer programmingdaunting should collaborate with an experienced computer programmer.2. Materials2.1. HardwareA personal computer or a computer cluster with a modern processor isrequired. The use of a computer cluster is always advised over a stand-alonemachine for reducing analysis and compute time.2.2. Software1. Operating system (OS): the use of UNIX or a UNIX-based OS such as Linux isadvocated over other common OS. If other systems are preferred, users shouldensure that the OS supports the ability to write, compile, and execute customgeneratedcode (see Note 1).2. The BLAST package: BLAST package (10) is required for the purposes ofsequence comparison. The BLAST package also includes precompiled binaries(“ready-to-run” programs) of various tools and utilities besides BLAST, and isavailable for download from the National Center for Biotechnology Information(NCBI) website for most commonly used OS (http://www.ncbi.nlm.nih.gov/BLAST/download.shtml). The NCBI version of BLAST differs from the WUWashington University-BLAST package (11) available from the WashingtonUniversity in St. Louis (http://blast.wustl.edu), both in implementation and results.Therefore, programs that parse BLAST output should be modified based on theversion used. This protocol assumes the use of the NCBI BLAST package.3. A programmatic wrapper: a wrapper program that is able to run BLAST searchessequentially for each protein in the query set is required (see Note 2). The wrapperprogram can be extended to include other steps in the protocol as well, such asparsing of BLAST results, and execute house-keeping tasks such as moving andstoring various data in proper directories and compressing output files. This programhas to be written by the user.4. BLAST results parser program: a program that is able to extract relevant informationfrom raw BLAST output (such as expectation values and start and stopcoordinates of the matching sequence span) is also required. Information relevantto each method is described in detail in Methods. Raw BLAST outputcould be subsequently discarded, or saved if disk space is inexpensive. The useris free to write a parser program or use parsing programs available over theInternet (see Note 2).5. Other required programs: computer programs are also needed for the followingtasks:a. Generating phylogenetic profiles using BLAST results.b. Comparing phylogenetic profiles and measuring profile similarity.c. Finding fusion proteins using BLAST results.