The obtained sequences were analyzed using the DNASTAR programs (DNASTAR, United States). Sequence alignments were generated with the Clustal W algorithm implemented in the MEGA 6.0.5 software (http://megasoftware.net).
Programs
Manufactured by DNASTAR
Sourced in United States
DNASTAR programs are bioinformatics software tools designed for DNA, RNA, and protein sequence analysis. These programs provide a range of functionalities, including sequence assembly, alignment, and visualization, as well as gene prediction and annotation. The core function of DNASTAR programs is to facilitate the analysis and interpretation of genetic data.
Automatically generated - may contain errors
Lab products found in correlation
2 protocols using programs
1
Sequence Alignment Using DNASTAR
2
Bioinformatic Analysis of Pacifastacus Prophenoloxidase-Activating Proteins
Check if the same lab product or an alternative is used in the 5 most similar protocols
PxPAPsand deduced amino acid sequences were analyzed using DNASTAR programs (version 5.02) (DNASTAR, Inc., Madison, WI). Signal peptide and domain prediction were performed by SMART (
http://smart.embl-heidelberg.de/ ). Translation of
PxPAPsand prediction of the deduced proteins were conducted with ExPASy (
http://www.au.expasy.org/ ). Homologous protein sequence comparisons with entries in the updated GenBank/EMBL, SWISS-PROT, and PIR databases were performed with Blast and PSI-Blast programs with an
E-value cut-off of 10
−8(Friedman and Hughes 2006). Sequence alignment was performed with ClustalX version 1.81 using default parameters (
Thompson et al. 1997 (link)
) and edited using GeneDoc (version 2.04) (Free Software Foundation, Inc., MA). Maximum parsimony (MP) method was used for phylogenetic analysis with Mega 5.1 (
Kumar et al. 2008 (link)
), and bootstrap analysis provided support values for the branches (
Felsenstein 1985 (link)
). Clip domain, catalytic residues, and substrate-specific residues of PxPAPs were predicted through a multiple alignment of homologous sequences.
+ Expand
PxPAPsand deduced amino acid sequences were analyzed using DNASTAR programs (version 5.02) (DNASTAR, Inc., Madison, WI). Signal peptide and domain prediction were performed by SMART (
PxPAPsand prediction of the deduced proteins were conducted with ExPASy (
E-value cut-off of 10
−8(Friedman and Hughes 2006). Sequence alignment was performed with ClustalX version 1.81 using default parameters (
Thompson et al. 1997 (link)
) and edited using GeneDoc (version 2.04) (Free Software Foundation, Inc., MA). Maximum parsimony (MP) method was used for phylogenetic analysis with Mega 5.1 (
Kumar et al. 2008 (link)
), and bootstrap analysis provided support values for the branches (
Felsenstein 1985 (link)
). Clip domain, catalytic residues, and substrate-specific residues of PxPAPs were predicted through a multiple alignment of homologous sequences.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!