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The first two are a natural consequence of most representations of alignments and their annotation being human-unreadable and best portrayed in the familiar sequence row and alignment column format, of which examples are widespread in the literature.
In bioinformatics and biochemistry, the FASTA format is a text-based format for representing either nucleotide sequences or amino acid (protein) sequences, in which nucleotides or amino acids are represented using single-letter codes.
The UCSC site hosts a set of genome analysis tools, including a full-featured GUI interface for mining the information in the browser database, a FASTA format sequence alignment tool BLAT [9] that is also useful for simply finding sequences in the massive sequence (human genome = 3.23 billion bases [Gb]) of any of the featured genomes.
Xournal is an open source tool for annotating PDF files. It supports pen , mouse , and keyboard input. [ 1 ] It and the related Xournal++ are commonly used for adding annotations and electronic signatures to PDF files, especially on Linux desktops.
SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM (Binary Alignment/Map) and CRAM formats, written by Heng Li.
PDF-XChange Viewer (now superseded by the PDF-XChange Editor) is a freemium PDF reader for Microsoft Windows. It supports saving PDF forms and importing or exporting form data in FDF/XFDF format. Since version 2.5, there has been partial support for XFA, and exporting form data in XML Data Package (XDP) or XML format.
deskUNPDF: PDF converter to convert PDFs to Word (.doc, docx), Excel (.xls), (.csv), (.txt), more; GSview: File:Convert menu item converts any sequence of PDF pages to a sequence of images in many formats from bit to tiffpack with resolutions from 72 to 204 × 98 (open source software) Google Chrome: convert HTML to PDF using Print > Save as PDF.
PDF Studio is a commercial desktop application from Qoppa Software to create, convert, review, annotate, and edit Portable Document Format (PDF) documents.