BioEdit v188.8.131.52 full – Phần mềm phân tích và sắp xếp chuỗi (Y sinh)
I. Giới thiệu
BioEdit là chương trình biên tập chuỗi và sắp xếp liên kết chuỗi . BioEdit được thiết kế để có thể xử lý hầu hết các chức năng chỉnh sửa và biên tập chuỗi đơn giản và liên kết mà các nhà nghiên cứu có thể thực hiện hàng ngày, cũng như một vài phân tích chuỗi cơ bản.
Video hướng dẫn sử dụng phần mềm BioEdit v184.108.40.206 full:
II. Những tính năng chính của phần mềm BioEdit v220.127.116.11 full
Tính năng chính (Tiếng Anh)
Four modes of manual alignment: select and slide, dynamic grab and drag, gap insert and delete by mouse click, and on-screen typing which behaves like a text editor.
In-color alignment and editing with separate nucleic acid and amino acid color tables and full control over background colors.
Plasmid drawing interface for automated creation of plasmid vector graphic from a DNA sequence. Easily mark positions, add features with arrows and curved boxes, and mark restriction enzyme cut sites. Also show detail of polylinker and draw moveable arrows and shapes with drawing tools.
Dynamic information-based alignment shading.
Point-and-click color table editing
Display and print ABI chromatograms with professional-looking output.
Group sequences into groups or families.
Lock alignment of grouped sequences for synchronized hand alignment adjustments.
Annotate sequences with graphical features with dynamic view in alignment windows including feature annotation information tooltips.
Lock sequences to prevent accidental edits.
Specify characters to be considered valid for calculations in amino acid and nucleotide sequences.
Sort sequences by name, LOCUS, DEFINITION, ACCESSION, PID/NID, REFERENCES, COMMENTS or by residue frequency in a selected column.
Merge alignments through a reference sequence.
Append one alignment to the end of another.
Rudimentary phylogenetic tree viewer (for phylip-format trees) that allows node flipping and printing.
Verbally read back sequences in single sequence editor to verify hand-typed sequence entries.
Reads and writes Genbank, Fasta, Phylip 3.2, Phylip 4, and NBRF/PIR formats. Now also reads GCG and Clustal formats
Utilizes Don Gilbert’s ReadSeq to automatically import and export 11 additional formats, including MSF, ASN.1, IG/Stanford and EMBL.
Allows import of compatible formats directly from the clipboard without saving to a file first.
Easy customization of menu shortcuts for editor window
RNA comparative analysis, including covariation, potential pairings and mutual information analysis (currently capable of generating matrices up to 10,000 x 10,000 — but this would be a 600+ Mb file) with matrix plotter for 2-D matrix output tables and area graphing for individual rows of a data matrix. Matrix plotter and line graphs both have point-and-click data selection and the matrix plotter and 1-D line graphs of matrix data are now dynamically linked
View sections of very large matrices with plotter (tested on up to a 5183 x 5183 matrix = 180 Mb file)
View and manipulate alignments up to 20,000 sequences.
Binary file format (BioEdit Project format) for fast open and save of large alignments — the 6205 sequences of the prokaryotic 16S rRNA alignment (29 Mb file) open and save in less than 10 sec on a 233 MHz Pentium.
ORF searching with user-defined preferences
Formatted translations of nucleic acid sequences with codon usage summary, choice of one- or three-letter amino acid codes, translation of selected region only of nucleic acid, and choice of start/stop codons
Split window view for simultaneous and synchronized editing of two different places in the same file — split window vertically or horizontally
Amino acid and nucleotide composition analyses and plots
Align protein-encoding nucleic acid sequences through amino acid translation.
ClustalW multiple sequence alignment (interface internal, external program by Des Higgins et. al.) with auto-update of aligned protein full titles and GenBank field information, as well as nucleotide coding sequence when aligned from a protein view of nucleotide sequences.
Protein hydrophobicity/hydrophilicity plots
Protein hydrophobic moment matrix plots (0-180 dgrees)
Full choice of system fonts now available in edit window
Restriction mapping with any or all-frame translation, multiple enzyme choice and output options, and circular DNA capability
Browse restriction enzymes by manufacturer
Sequences at least 4.6 Mb in length can be manipulated (the largest sequence tested so far is the E. coli genome (4.6 Mb) — E. coli was opened, reverse complemented, translated into 10,125 codon stretches >=100 amino acids, and opened and saved with full GenBank annotation).
Six-frame translations capable of raw translation of entire genomes (tested with the E. coli genome — ca. 4.6 Mb)
Save GenBank format Entrez files with LOCUS, DEFINITION, ACCESSION, PID, NID, DBSOURCE, KEYWORDS, SOURCE, REFERENCE, COMMENT, and FEATURES fields intact. Modify or add your own information. Multiple sequence files saved in GenBank format retain any entered information. This information is also saved in the BioEdit Project file format.
Configure and run accessory applications via the BioEdit graphical application configuration interface. BioEdit currently comes with:
TreeView (install package — install separately)
Phylip programs including:
Full NCBI package of local BLAST programs, database creation, and internet BLAST client 2.0, with sample protein database of E. coli open reading frames.
Shaded graphical output with identity and similarity (for protein) shading and several formatting options.
Rich text export of formatted, shaded alignments
On-line help system (always a couple of versions behind the program).
Máy tính i486 + tương thích với PC chạy Windows 95, 98, NT hoặc 2000 / 7. Bạn nên sử dụng pentium có RAM tối thiểu 32 Mb. Khoảng 30 – 40 Mb dung lượng đĩa trống cũng được yêu cầu (cài đặt BioEdit sẽ mất 15 Mbyte, nhưng thư mục tạm thời yêu cầu khoảng 15 Mb và tệp BioEdit.zip mất 8 Mb).