BLAST+ executables
Do you have difficulties running high volume BLAST searches? Do you have proprietary sequence data to search and cannot use the NCBI BLAST web site? Do you have access to your own server? Do you have your own research pipeline? Have security or IP concerns about sending searches outside of your organization? If you answered yes to any of these questions, read on!
Curl is a command line tool and library. It is open source and run on various OS. Basically it is used to transferring data from a server to another server. It supports many types of Protocol like FTP, SFTP, POP3 SMB, SMTP, SMTPS, DICT, FILE, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3S, RTMP, RTSP, SCP.
FTP was removed in macOS High Sierra and macOS Mojave, but ftp and ftp server do remain in older versions of Mac OS and Mac OS X system software, even if the ftp server has to be manually activated with launchctl. In some older versions of Mac OS, you can even connect with ftp from the Finder however. SmartFTP is an FTP (File Transfer Protocol), FTPS, SFTP, WebDAV, Amazon S3, Backblaze B2, Google Drive, OneDrive, SSH, Terminal client. It allows you to transfer files between your local computer and a server on the Internet. With its many basic and advanced Features SmartFTP also offers secure, reliable and efficient transfers that make it a.
The NCBI provides a suite of command-line tools to run BLAST called BLAST+. This allows users to perform BLAST searches on their own server without size, volume and database restrictions. BLAST+ can be used with a command line so it can be integrated directly into your workflow.
What are the next steps?
Download and install BLAST+. Installers and source code are available from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/. Download the databases you need,(see database section below), or create your own. Start searching.
For more details, please see the BLAST+ user manual, the BLAST Help manual, the BLAST releases notes, and the article in BMC Bioinformatics (PubMed link). See our versioning policy.
The BLAST+ suite is the currently supported package. The older C toolkit executables are no longer supported. See our versioning policy.
We are always listening and welcome your feedback at BLAST Support Center.
Magic-BLAST
Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Read more about Magic-BLAST at https://ncbi.github.io/magicblast.
Installers and source code are available from ftp://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/LATEST.
IgBLAST
IgBLAST facilitates the analysis of immunoglobulin and T cell receptor variable domain sequences. For details please see the documentation at https://ncbi.github.io/igblast/ and the article in Nucleic Acids Research (https://www.ncbi.nlm.nih.gov/pubmed/23671333).
Installers and source code are available from ftp://ftp.ncbi.nih.gov/blast/executables/igblast/release/LATEST.
SRPRISM
SRPRISM is a short read alignment tool that works with genomic sequences and handles alternative loci. For more information, see ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/srprism/README. A LINUX executable is available under ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/srprism
Databases
BLAST databases are updated daily and may be downloaded via FTP fromftp://ftp.ncbi.nlm.nih.gov/blast/db/.Database sets may be retrieved automatically with update_blastdb.pl, which is part of the BLAST+ suite.Please refer to the BLAST database documentation for more details.
The NCBI makes searchable collection of position-specific scoring matrices that can be used for sensitive protein and translated nucleotide searches. These are known as the Conserved Domain Database and can be searched with the RPSBLAST and RPSTBLASTN executables distributed with the BLAST+ package. The most comprehensive collection of CDD's is available at ftp://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/little_endian/Cdd_NCBI_LE.tar.gz. Subsets of the comprehensive collection are available at ftp://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/little_endian/. Documentation on these CDD collections is available at ftp://ftp.ncbi.nlm.nih.gov/pub/mmdb/cdd/README.
In this article, I will demonstrate what is curl and how can we use curl? So, let’s begin the journey of curl.
What is Curl?
Curl is a command line tool and library. It is open source and run on various OS. Basically it is used to transferring data from a server to another server. It supports many types of Protocol like FTP, SFTP, POP3 SMB, SMTP, SMTPS, DICT, FILE, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3S, RTMP, RTSP, SCP. Curl also support SSL certificate. In today world, most of the equipment uses curl. Latest version of curl is 7.44.0 that released on 12th August 2015.
Download
You can download curl as per your Operating system compatible. It can be x86 or x64 as per your requirement. You can download it from here.
There are various protocols where we can use curl. But today I will explain you how to work with FTP and SFTP using curl.
Curl with FTP
FTP, means “File Transfer Protocol, in short we use FTP, is a standard network protocol that is used to transfer the data from one host to another host over a TCP based network like Internet.
You can use following command with FTP.
Login usign curl on FTP
Upload using curl on FTP
Download using curl on FTP
Rename using curl on FTP
Delete using curl on FTP
Make directory using curl on FTP
Remove directory using curl on FTP
Curl with SFTP
SFTP, means “SSH File Transfer Protocol, or “Secure File Transfer Protocol”, in short we use SFTP, is a standard network protocol that is used to transfer the data from one host to another host over a secure connection.
Mac Ftp Server
You can use following command with SFTP.
Login using curl on SFTP
Upload using curl on SFTP
Download using curl on SFTP
Rename using curl on SFTP
Delete using curl on SFTP
Make directory using curl on SFTP
Remove directory using curl on SFTP
References
Ftp Client Software For Mac
Conclusion:
Mac Os Ftp Client
So, Today we learned how to use curl command line tool with ftp and sftp to transfer the file or data from local to ftp and sftp.
How To Download From Ftp Site On Mac
I hope this post will help you. Please put your feedback using comment which helps me to improve myself for next post. If you have any doubts please ask your doubts or query in the comment section and If you like this post, please share it with your friends. Thanks