July 2003
Intermediate to advanced
368 pages
13h 44m
English
Content preview from BLAST
Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
O’Reilly covers everything we've got, with content to help us build a world-class technology community, upgrade the capabilities and competencies of our teams, and improve overall team performance as well as their engagement.I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.
This is the Title of the Book, eMatter Edition
Copyright © 2012 O’Reilly & Associates, Inc. All rights reserved.
Command-Line Tutorial
|
185
You should see the following output:
>AU109017 AU109017 Caenorhabditis elegans cDNA clone:yk701g7 : 5' end, single read.
TGGCCTACTGGGGTTTAATTACCCAAGTTTGAGATGGCTGCTGCTTCAGTGAAAGGCTTT
TTCCAGCGGACCGGAATCAGCATCAAAGAATATTTTAAACGAATGGGAAATGATTATGCT
ACTGTAGCTAGGGAAACTGTCCAAGGATGTAAAGATAGACCTGTTAAAGCTGGAGTTGTT
TTCTCTGGGCTCGGTTTTTTAACCTATGCATATCAGACAAATCCAACAGAGCTGGAAATG
TATGATTATTTATGCGAGAGACGACAAAAGTTAGTTTTGGTCCCGAATTCTGAGCATAAT
CCGGCTACAACTAAAGAATTAACTGCTCGCGA
And for proteins, you can rely on a similar action:
xdget -p globins HBP_CANLI
You should see the following output:
>HBP_CANLI P42511 Leghemoglobin.
MGAFSEKQESLVKSSWEAFKQNVPHHSAVFYTLILEKAPAAQNMFSFLSNGVDPNNPKLK
AHAEKVFKMTVDSAVQLRAKGEVVLADPTLGSVHVQKGVLDPHFLVVKEALLKTFKEAVG
DKWNDELGNAWEVAYDELAAAIKKAMGSA
nrdb and patdb
The nrdb and patdb programs are useful for removing the redundant sequences you
saw earlier. Use nrdb first:
nrdb globins > globins_nr
The additional output from the program is as follows:
--------- Records --------- -------------- Residues -----------
Database Read Duplicate Written Read Duplicate Written
globins 1203 39 1164 211,084 37,819 173,265
Totals: 1203 39 1164 211,084 37,819 173,265
No. of base word hits: 53 (53 total)
No. of 32-bit hash hits: 39
Total memory allocated: 0.500 MB
Longest comment line ...
Become an O’Reilly member and get unlimited access to this title plus top books and audiobooks from O’Reilly and nearly 200 top publishers, thousands of courses curated by job role, 150+ live events each month,
and much more.
Read now
Unlock full access
More than 5,000 organizations count on O’Reilly
O’Reilly covers everything we've got, with content to help us build a world-class technology community, upgrade the capabilities and competencies of our teams, and improve overall team performance as well as their engagement.Julian F.
I wanted to learn C and C++, but it didn't click for me until I picked up an O'Reilly book. When I went on the O’Reilly platform, I was astonished to find all the books there, plus live events and sandboxes so you could play around with the technology.Addison B.
I’ve been on the O’Reilly platform for more than eight years. I use a couple of learning platforms, but I'm on O'Reilly more than anybody else. When you're there, you start learning. I'm never disappointed.Amir M.
I'm always learning. So when I got on to O'Reilly, I was like a kid in a candy store. There are playlists. There are answers. There's on-demand training. It's worth its weight in gold, in terms of what it allows me to do.