BOL: Related items

Basics of BLAST Programs !

BioStar — Fri, 26 Jul 2024 06:04:26 -0500

The Basic Local Alignment Search Tool (BLAST) is a powerful bioinformatics program used to compare an input sequence (such as DNA, RNA, or protein sequences) against a database of sequences to find regions of similarity. Developed by the National Center for Biotechnology Information (NCBI), BLAST is widely used for identifying species, finding functional and evolutionary relationships between sequences, and predicting the function of novel sequences.

Key Features of BLAST:
1. Sequence Comparison: BLAST searches for local alignments between the query sequence and sequences in a database. It identifies regions of similarity, which can help infer functional and evolutionary relationships.

2. Speed and Efficiency: BLAST uses heuristic algorithms, making it faster than exhaustive search methods, suitable for large-scale database searches.

3. Versatility: There are several versions of BLAST for different types of sequence comparisons:
- blastn: Compares a nucleotide query sequence against a nucleotide sequence database.
- blastp: Compares a protein query sequence against a protein sequence database.
- blastx: Compares a nucleotide query sequence translated in all reading frames against a protein sequence database.
- tblastn: Compares a protein query sequence against a nucleotide sequence database translated in all reading frames.
- tblastx: Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database.

4. Scoring and E-value: BLAST results are scored based on the quality and length of the alignments. The E-value (expect value) indicates the number of alignments one can expect to find by chance, with lower E-values representing more significant matches.

5. Output Formats: BLAST provides results in various formats, including plain text, HTML, XML, and JSON, making it adaptable for different types of analyses and integrations with other tools.

Applications of BLAST:
- Genomic Research: Identifying genes, understanding genetic diversity, and mapping genome sequences.
- Protein Function Prediction: Inferring the function of unknown proteins by comparing them to known protein sequences.
- Evolutionary Studies: Exploring evolutionary relationships between organisms by comparing their genetic material.
- Medical Research: Identifying pathogens, understanding disease mechanisms, and developing treatments by comparing sequences of interest.

Overall, BLAST is an essential tool in bioinformatics, offering a reliable and efficient way to analyze and interpret biological sequence data.

FSA: Fast Statistical Alignment

Jit — Mon, 06 Feb 2017 04:26:01 -0600

FSA is a probabilistic multiple sequence alignment algorithm which uses a "distance-based" approach to aligning homologous protein, RNA or DNA sequences. Much as distance-based phylogenetic reconstruction methods like Neighbor-Joining build a phylogeny using only pairwise divergence estimates, FSA builds a multiple alignment using only pairwise estimations of homology. This is made possible by the sequence annealing technique for constructing a multiple alignment from pairwise comparisons, developed by Ariel Schwartz in "Posterior Decoding Methods for Optimization and Control of Multiple Alignments."

FSA brings the high accuracies previously available only for small-scale analyses of proteins or RNAs to large-scale problems such as aligning thousands of sequences or megabase-long sequences. FSA introduces several novel methods for constructing better alignments:

FSA uses machine-learning techniques to estimate gap and substitution parameters on the fly for each set of input sequences. This "query-specific learning" alignment method makes FSA very robust: it can produce superior alignments of sets of homologous sequences which are subject to very different evolutionary constraints.
FSA is capable of aligning hundreds or even thousands of sequences using a randomized inference algorithm to reduce the computational cost of multiple alignment. This randomized inference can be over ten times faster than a direct approach with little loss of accuracy.
FSA can quickly align very long sequences using the "anchor annealing" technique for resolving anchors and projecting them with transitive anchoring. It then stitches together the alignment between the anchors using the methods described above.
The included GUI, MAD (Multiple Alignment Display), can display the intermediate alignments produced by FSA, where each character is colored according to the probability that it is correctly aligned (see the picture and movie at the top of the page).

You can see more information on the FAQ.

Address of the bookmark: http://fsa.sourceforge.net/

Salzberg lab

Mon, 15 May 2017 05:14:01 -0500

We are a computational biology lab that develops novel methods for analysis of DNA and RNA sequences. Our research includes software for aligning and assembling RNA-seq data, whole-genome assembly, and microbiome analysis. We work closely with biomedical scientists to apply these methods to current problems arising in a broad spectrum of biological and medical research areas. We’re also part of the Center for Computational Biology, a group of 20+ faculty members and their labs at Johns Hopkins working on computational, statistical, and mathematical methods that can turn massive genomic data sets into biologically and clinically useful information.

https://salzberg-lab.org/

Gblocks: eliminates poorly aligned positions and divergent regions of a DNA or protein alignment

Poonam Mahapatra — Sat, 02 Jun 2018 07:36:05 -0500

Gblocks eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis. This server implements the most important features of the Gblocks program to make its use as simple as possible without loosing the functionality that it is necessary in most of the cases. Other options can be changed in the stand-alone program. You can see here an example output file showing the blocks selected from a protein alignment. Further information can be found in the online documentation.

Address of the bookmark: http://molevol.cmima.csic.es/castresana/Gblocks_server.html

MutaBind

Jit — Mon, 06 Jun 2016 13:34:09 -0500

MutaBind is a new computational method and server created through NCBI research efforts that maps mutations on a protein structural complex, calculates changes in binding affinity, identifies deleterious mutations and produces a downloadable mutant structural model. http://www.ncbi.nlm.nih.gov/projects/mutabind/index.fcgi/

MutaBind guides you through this process, step by step, starting with selecting a protein complex and inputting PDB code or uploading PDB files. You can also retrieve results with a job ID number, view help documents, and review the MutaBind method and references.

More at http://www.ncbi.nlm.nih.gov/projects/mutabind/index.fcgi/

NCBI PSI-BLAST Tutorial

Fri, 23 Aug 2013 02:25:02 -0500

http:--www.biotechnology.jhu.edu- Tutorial for PSI-BLAST, an extension of BLAST that uses matrix algebra. BLAST is a cornerstone bioinformatics tool at NCBI. BLAST is the Basic Local Alignment Search tool and will protein and DNA sequences that are related to a sequence that the user provides.

YASS :: genomic similarity search tool

Jit — Mon, 02 May 2016 09:26:00 -0500

YASS is a genomic similarity search tool, for nucleic (DNA/RNA) sequences in fasta or plain text format (it produces local pairwise alignments). Like most of the heuristic pairwise local alignment tools for DNA sequences (FASTA, BLAST, PATTERNHUNTER, BLASTZ/LASTZ, LAST ...), YASS uses seeds to detect potential similarity regions, and then tries to extend them to local alignments. This genomic search tool uses multiple transition constrained spaced seeds that enable to search more fuzzy repeats, as non-coding DNA/RNA. Another simple, but interesting feature is that you can specify the seed pattern used in the search step (as provided for example by iedera).

Main features of YASS are:

multiple, possibly overlapping seeds and a new hit criterion to ensure a good sensitivity/selectivity trade-off
transition-constrained spaced seeds to improve sensitivity (transition mutations are purine to purine [A<->G] or pyrimidine to pyrimidine [C<->T])
using different scoring schemes with bit-score and E-value evaluated according to the sequence background frequencies
parameterizable output filter for low complexity repeats
reporting of various alignment statistical parameters (mutation bias along triplets, transition/transversion)
post-processing step to group gapped alignments

Address of the bookmark: http://bioinfo.lifl.fr/yass/

Mauve: a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion

Jit — Sat, 24 Dec 2016 09:20:53 -0600

Mauve is a system for constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignments provide a basis for research into comparative genomics and the study of genome-wide evolutionary dynamics.

Mauve has been developed with the idea that a multiple genome aligner should require only modest computational resources. It employs algorithmic techniques that scale well in the lengths of sequences being aligned. For example, a pair of Y. pestis genomes can be aligned in under a minute, while a group of 9 divergent Enterobacterial genomes can be aligned in a few hours. However, the current algorithm’s compute time (progressiveMauve) scales cubically in the number of genomes to align, making it unsuitable for datasets containing more than 50-100 bacterial genomes.

Address of the bookmark: http://darlinglab.org/mauve/mauve.html

Laj: viewing and manipulating the output from pairwise alignment programs

Abhimanyu Singh — Wed, 01 Mar 2017 08:35:40 -0600

Laj is a tool for viewing and manipulating the output from pairwise alignment programs such as blastz. It can display interactive dotplot, pip, and text representations of the alignments, a diagram showing the locations of exons and repeats, and annotation links to other web sites containing additional information about particular regions.

The program is written in Java in order to provide a graphical user interface that is portable across a variety of computer platforms; indeed its name stands for "Local Alignments with Java". Currently it exists in two forms, a stand-alone application and a web-based applet, with slightly different capabilities.

Address of the bookmark: http://www.bx.psu.edu/~ratan/

A Post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs

Abhimanyu Singh — Fri, 12 May 2017 10:50:29 -0500

PAGIT addresses the need for software to generate high quality draft genomes. It is based on a series of programs that we developed:

ABACAS, that is able to contiguate contigs from a de novo assembly against a closely related reference.

IMAGE, an iterative approach for closing gaps in assembled genomes using mate pair information. It is able to close gaps left open by the assembler in a draft genome, even when using the same data sets as used by the original assembler.

iCORN, that enables errors in the consensus sequence to be corrected by iteratively mapping reads to the current assembly. An improved version, especially correction Pacfic Bioscience assemblies (PacBio) can be found here.

RATT, a tool to transfer the annotation from a reference genome, or an earlier assembly, onto the latest assembly.

PAGIT bundles these software and makes them more accessible for users.

Address of the bookmark: http://www.sanger.ac.uk/science/tools/pagit