COMBOSA3D: combining sequence alignments with three-dimensional structures

نویسنده

  • P. M. Stothard
چکیده

UNLABELLED COMBOSA3D is a program that allows sequence conservation to be viewed in its proper three-dimensional environment. It superimposes sequence alignment information onto a protein structure using a customizable color scheme, which is also applied to a textual sequence alignment for reference. AVAILABILITY The program can be tested at http://www.bioinformatics.org/combosa3d/, and the source code is freely available.

برای دانلود رایگان متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

PALI: a database of alignments and phylogeny of homologous protein structures

PALI is a database of structure-based sequence alignments and phylogenetic relationships derived on the basis of three-dimensional structures of homologous proteins. This database enables grouping of pairs of homologous protein structures on the basis of their sequence identity calculated from the structure-based alignment and PALI also enables association of a new sequence to a family and auto...

متن کامل

3DCoffee: combining protein sequences and structures within multiple sequence alignments.

Most bioinformatics analyses require the assembly of a multiple sequence alignment. It has long been suspected that structural information can help to improve the quality of these alignments, yet the effect of combining sequences and structures has not been evaluated systematically. We developed 3DCoffee, a novel method for combining protein sequences and structures in order to generate high-qu...

متن کامل

LETTER TO THE EDITOR The RNA structure alignment ontology

Multiple sequence alignments are powerful tools for understanding the structures, functions, and evolutionary histories of linear biological macromolecules (DNA, RNA, and proteins), and for finding homologs in sequence databases. We address several ontological issues related to RNA sequence alignments that are informed by structure. Multiple sequence alignments are usually shown as two-dimensio...

متن کامل

Multiple Sequence Alignment Using Three- Dimensional Fragments

Background: Dialign is a DNA/Protein alignment tool for performing pairwise and multiple pairwise alignments through the comparison of gap-free segments (fragments) between sequence pairs. An alignment of two sequences is a chain of fragments, i.e local gap-free pairwise alignments, with the highest total score. METHOD: A new approach is defined in this article which relies on the concept of us...

متن کامل

SAD - a normalized structural alignment database: improving sequence-structure alignments

MOTIVATION We present a structural alignment database that is specifically targeted for use in derivation and optimization of sequence-structure alignment algorithms for homology modeling. We have paid attention to ensure that fold-space is properly sampled, that the structures involved in alignments are of significant resolution (better than 2.5 A) and the alignments are accurate and reliable....

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

عنوان ژورنال:
  • Bioinformatics

دوره 17 2  شماره 

صفحات  -

تاریخ انتشار 2001