Constructing and refining multiple sequence alignments with PileUp, SeqLab, and the GCG suite [0.03%]
PileUp、SeqLab和GCG软件包的多重序列联配的建立与修改方法
Steven M Thompson
Steven M Thompson
This unit discusses how the Accelrys GCG Wisconsin Package SeqLab graphical user interface can be used to align, annotate, analyze, and export into alternative formats, multiple biological sequence data. The emphasis is on discovering and r...
Finding homologs in amino acid sequences using network BLAST searches [0.03%]
基于网络BLAST搜索的氨基酸序列同源性查找方法
Istvan Ladunga
Istvan Ladunga
BLAST, Basic Local Alignment Search Tool is used more frequently than any other biosequence database search program. The purpose of this unit is not only to show how to run searches on the Web, but also to demonstrate how to fine-tune argum...
Robert Finn,Sam Griffiths-Jones,Alex Bateman
Robert Finn
Pfam is a database of such protein domain families, with each family represented by multiple sequence alignments and profile hidden Markov models (HMMs). In addition, each family has associated annotation, literature references and links to...
David Gordon
David Gordon
Consed is a program for viewing and editing assemblies prepared by the Phrap assembly program. This unit presents a general introduction to Consed. It also provides instructions for identifying problem regions and searching in Consed. Addit...
Large scale sequencing [0.03%]
大规模测序
Lincoln Stein
Lincoln Stein
DNA sequencing and assembly is the Philosopher's Stone of bioinformatics, where the raw material of wet lab enzymatic chemistry is transformed into the bits and bytes of sequence information. The sequence information becomes the foundation ...
Arthur L Delcher,Steven L Salzberg,Adam M Phillippy
Arthur L Delcher
The MUMmer sequence alignment package is a suite of computer programs designed to detect regions of homology in long biological sequences. Version 2.1 makes several improvements to the package, including: increased speed and reduced memory ...
PipMaker: a World Wide Web server for genomic sequence alignments [0.03%]
PIPMAKER：一个用于基因组序列比对的动态网页服务器
Laura Elnitski,Cathy Riemer,Scott Schwartz et al.
Laura Elnitski et al.
PipMaker is a World-Wide Web site used to compare two long genomic sequences and identify conserved segments between them. This unit describes the use of the PipMaker server and explains the resulting output files. PipMaker provides an effi...
Roderic D M Page
Roderic D M Page
Comparisons of whole genomes can yield important insights into the evolution of genome structure, such as the role of inversions in bacterial evolution and the identification of large-scale duplications in the human genome. This unit briefl...
Yuandan Lee,John Quackenbush
Yuandan Lee
The TIGR Gene Index web pages provide access to analyses of ESTs and gene sequences for nearly 60 species, as well as a number of resources derived from these. Each species-specific database is presented using a common format with a homepag...
Don Gilbert
Don Gilbert
One of the major challenges in using bioinformatics software is that there are a wide variety of sequence formats, e.g., GenBank, EMBL, and FASTA. It is often the case that a sequence or a set of sequences is in one format but is needed in ...