BOL: Related items

HS3D: Homo Sapiens Splice Sites Dataset

Jit — Fri, 12 Jun 2020 12:33:17 -0500

HS3D (Homo Sapiens Splice Sites Dataset) is a data set of Homo Sapiens Exon, Intron and Splice regions extracted from GenBank Rel.123. The aim of this data set is to give standardized material to train and to assess the prediction accuracy of computational approaches for gene identification and characterization. From the complete GenBank (Primate Sequences Division) Rel.123 (162,557 entries), entries of Human Nuclear DNA including Complete CDS and more than one Exon have been selected, and 4523 exons and 3802 introns have been extracted from these entries. Details about extracted exons and introns are reported (Locus, number, Start and End position in the entry, sequence, length, G+C content, presence of not AGCT data (nucleotide scan check)). Statistics are also reported (overall nucleotides, average G+C content, nucleotide scan check results, number of not GT starting / AG ending introns, minimum / maximum / average length, length standard deviation) . 3799+3799 donor and acceptor sites, as windows of 140 nucleotides around each splice site have been extracted. After discarding sequences not including canonical GT–AG junctions (65+74), including insufficient data (not enough material for a 140 nucleotide window) (686+589), including not AGCT bases (29+30), and redundant (218+226) there are 2796+ 2880 windows.

1. P.Pollastro, S.Rampone (2002). HS3D, a Dataset of Homo Sapiens Splice Regions, and its Extraction Procedure from a Major Public Database , International Journal of Modern Physics C, 13(8), 1105-1117. (please cite this paper)

2. P.Pollastro, S.Rampone (2003). HS3D: Homo Sapiens Splice Site Data Set , Nucleic Acids Research, 2003 Annual Database Issue.

Address of the bookmark: http://www.sci.unisannio.it/docenti/rampone/

Ley Lab !

Fri, 11 Sep 2026 13:21:10 -0500

Research Program aims to elucidate how gut microbial species relate to genotypic differences between human individuals, to identify bacterial and archaeal species that share an evolutionary history with humans, and to determine the molecular basis of long-term host-microbial relationships. We approach these aims through a combination of population-level observations and laboratory-based molecular-level investigations. We link inter-microbial and microbial-host interactions at the molecular scale to patterns at population and evolutionary scales.

More at https://leylab.com/

HumCFS: a database of fragile sites in human chromosomes

Abhimanyu Singh — Sun, 21 Apr 2019 20:17:29 -0500

Fragile sites are specific chromosomal region that exhibit an increased frequency of chromosdomal breakge when cells are exposed to replicative stress. Since from the discovery of chromosomal fragile sites/regions (CFS), several line of evidence suggests their involvement in human pathologies and they have been recognized as a preferential site for integration of exogenous oncogenic DNA viruses and hotspots for chromosomal re-arrangement. There is large gap in our knowledge of human CFS region as knowledge about CFS are unequally distributed in literature, which impose a problem in studying these region. In order to address these issues, we develop this platform HumCFS, which provides comprehensive information about experimentally identified CFS at a single source.

https://link.springer.com/epdf/10.1186/s12864-018-5330-5?author_access_token=ICASEpyMAQaxLlKw--fyCG_BpE1tBhCbnbw3BuzI2RMA57KLmXk5bZabRUiDQzRFHXd6hjm4kWSiLV3mU5XVMitqXUwFMSo4x5vbfty0EDQ9PW1sd1h923_TYXkvJ5niSwAyZ7BklJ0ujFAFhcKtjw%3D%3D

Address of the bookmark: https://webs.iiitd.edu.in/raghava/humcfs/

Perl Special Vars Quick Reference

Abhimanyu Singh — Tue, 07 Feb 2017 05:08:47 -0600

`$_`	The default or implicit variable.
`@_`	Subroutine parameters.
`$a` `$b`	sort comparison routine variables.
`@ARGV`	The command-line args.
Regular Expressions
`$`	Regexp parenthetical capture holders.
`$&`	Last successful match (degrades performance).
`${^MATCH}`	Similar to `$&` without performance penalty. Requires /p modifier.
$`	Prematch for last successful match string (degrades performance).
`${^PREMATCH}`	Similar to $` without performance penalty. Requires `/p` modifier.
`$'`	Postmatch for last successful match string (degrades performance).
`${^POSTMATCH}`	Similar to `$'` without performance penalty. Requires `/p` modifier.
`$+`	Last paren match.
`$^N`	Last closed paren match (last submatch).
`@+`	Offsets of ends of successful submatches in scope.
`@-`	Offsets of starts of successful submatches in scope.
`%+`	Like `@+`, but for named submatches.
`%-`	Like `@-`, but for named submatches.
`$^R`	Last regexp (?{code}) result.
`${^RE_DEBUG_FLAGS}`	Current value of regexp debugging flags. See `use re 'debug';`
`${^RE_TRIE_MAXBUF}`	Control memory allocations for RE optimizations for large alternations.
Encoding
`${^ENCODING}`	The object reference to the Encode object, used to convert the source code to Unicode.
`${^OPEN}`	Internal use: \0 separated Input / Output layer information.
`${^UNICODE}`	Read-only Unicode settings.
`${^UTF8CACHE}`	State of the internal UTF-8 offset caching code.
`${^UTF8LOCALE}`	Indicates whether UTF8 locale was detected at startup.
IO and Separators
`$.`	Current line number (or record number) of most recent filehandle.
`$/`	Input record separator.
`$\|`	Output autoflush. 1=autoflush, 0=default. Applies to currently selected handle.
`$,`	Output field separator (lists)
`$\`	Output record separator.
`$"`	Output list separator. (interpolated lists)
`$;`	Subscript separator. (Use a real multidimensional array instead.)
Formats
`$%`	Page number for currently selected output channel.
`$=`	Current page length.
`$-`	Number of lines left on page.
`$~`	Format name.
`$^`	Name of top-of-page format.
`$:`	Format line break characters
`$^L`	Form feed (default "\f").
`$^A`	Format Accumulator
Status Reporting
`$?`	Child error. Status code of most recent system call or pipe.
`$!`	Operating System Error. (What just went 'bang'?)
`%!`	Error number hash
`$^E`	Extended Operating System Error (Extra error explanation).
`$@`	Eval error.
`${^CHILD_ERROR_NATIVE}`	Native status returned by the last pipe close, backtick (`` ) command, successful call to wait() or waitpid(), or from the system() operator.
ID's and Process Information
`$$`	Process ID
`$<`	Real user id of process.
`$>`	Effective user id of process.
`$(`	Real group id of process.
`$)`	Effective group id of process.
`$0`	Program name.
`$^O`	Operating System name.
Perl Status Info
`$]`	Old: Version and patch number of perl interpreter. Deprecated.
`$^C`	Current value of flag associated with -c switch.
`$^D`	Current value of debugging flags
`$^F`	Maximum system file descriptor.
`$^I`	Value of the -i (inplace edit) switch.
`$^M`	Emergency Memory pool.
`$^P`	Internal variable for debugging support.
`$^R`	Last regexp (?{code}) result.
`$^S`	Exceptions being caught. (eval)
`$^T`	Base time of program start.
`$^V`	Perl version.
`$^W`	Status of -w switch
`${^WARNING_BITS}`	Current set of warning checks enabled by `use warnings;`
`$^X`	Perl executable name.
`${^GLOBAL_PHASE}`	Current phase of the Perl interpreter.
`$^H`	Internal use only: Hook into Lexical Scoping.
`%^H`	Internaluse only: Useful to implement scoped pragmas.
`${^TAINT}`	Taint mode read-only flag.
`${^WIN32_SLOPPY_STAT}`	If true on Windows `stat()` won't try to open the file.
Command Line Args
`ARGV`	Filehandle iterates over files from command line (see also `<>`).
`$ARGV`	Name of current file when reading <>
`@ARGV`	List of command line args.
`ARGVOUT`	Output filehandle for -i switch
Miscellaneous
`@F`	Autosplit (-a mode) recipient.
`@INC`	List of library paths.
`%INC`	Keys are filenames, values are paths to modules included via `use, require,` or `do`.
`%ENV`	Hash containing current environment variables
`%SIG`	Signal handlers.
`$[`	Array and substr first element (Deprecated!).

See perlvar for detailed descriptions of each of these (and a few more) special variables.

pbalign: maps PacBio reads to reference sequences and saves alignments to a BAM file

Jit — Thu, 24 May 2018 10:06:52 -0500

pbalign aligns PacBio reads to reference sequences, filters aligned reads according to user-specific filtering criteria, and converts the output to either the SAM format or PacBio Compare HDF5 (e.g., .cmp.h5) format. The output Compare HDF5 file will be compatible with Quiver if --forQuiver option is specified.

Address of the bookmark: https://github.com/PacificBiosciences/pbalign