OnWorks favicon

formatrpsdb - Online in the Cloud

Run formatrpsdb in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command formatrpsdb that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator



formatrpsdb - Build databases for RPS Blast


formatrpsdb [-] [-E N] [-G N] [-S X] [-U str] [-b] [-f X] -i filename [-l filename]
[-n str] [-o] [-t str] [-v N]


Formatrpsdb is a utility that converts a collection of input sequences into a database
suitable for use with Reverse Position Specific (RPS) Blast. Each input sequence,
together with its position-specific scoring matrix (PSSM), is ASN.1 encoded into a
PssmWithParameters (or `scoremat') object and resides in a separate file. Scoremat
objects can be created using blastpgp. Formatrpsdb is given a list of these files and
produces the corresponding database.

Formatrpsdb is designed to perform the work of formatdb, makemat and copymat
simultaneously, without generating the large number of intermediate files these utilities
would need to create an RPS Blast database. Further, scoremat objects are in more general
use than the binary format makemat requires. It is hoped that direct manipulation of
scoremat objects will encourage conversion of more diverse sequence collections into RPS
Blast databases.

Databases generated by formatrpsdb are binary compatible with databases generated by
formatdb/makemat/copymat, although the database files will in general not be byte- for-
byte identical.


A summary of options is included below.

- Print usage message

-E N The gap extension penalty (if not specified in the scoremat; default = 1)

-G N The gap opening penalty (if not specified in the scoremat; default = 11)

-S X For scoremats that contain only residue frequencies, the scaling factor to apply
when creating PSSMs (default = 100)

-U str Underlying score matrix (if not specified in the scoremat; default = BLOSUM62)

-b Scoremat files are binary (vs. text) ASN1.

-f X Threshold for extending hits for RPS database (default = 11)

-i filename
Input file containing list of ASN.1 Scoremat filenames

-l filename
Log file name (default = formatrpsdb.log)

-n str Base name of output database (same as input file if not specified)

-o Create index files for database

-t str Title for database file

-v N Database volume size in millions of letters (default = 0, which really means no

Use formatrpsdb online using onworks.net services

Free Servers & Workstations

Download Windows & Linux apps

  • 1
    Image Downloader
    Image Downloader
    Crawl and download images using
    Selenium Using python3 and PyQt5.
    Supported Search Engine: Google, Bing,
    Baidu. Keywords input from the keyboard
    or input from ...
    Download Image Downloader
  • 2
    Eclipse Tomcat Plugin
    Eclipse Tomcat Plugin
    The Eclipse Tomcat Plugin provides
    simple integration of a tomcat servlet
    container for the development of java
    web applications. You can join us for
    Download Eclipse Tomcat Plugin
  • 3
    WebTorrent Desktop
    WebTorrent Desktop
    WebTorrent Desktop is for streaming
    torrents on Mac, Windows or Linux. It
    connects to both BitTorrent and
    WebTorrent peers. Now there's no
    need to wait for...
    Download WebTorrent Desktop
  • 4
    GenX is a scientific program to refine
    x-ray refelcetivity, neutron
    reflectivity and surface x-ray
    diffraction data using the differential
    evolution algorithm....
    Download GenX
  • 5
    PSPP is a program for statistical
    analysis of sampled data. It is a free
    replacement for the proprietary program
    SPSS. PSPP has both text-based and
    graphical us...
    Download pspp4windows
  • 6
    Git Extensions
    Git Extensions
    Git Extensions is a standalone UI tool
    for managing Git repositories. It also
    integrates with Windows Explorer and
    Microsoft Visual Studio
    (2015/2017/2019). Th...
    Download Git Extensions
  • More »

Linux commands